Itineray help: First trip to Japan (17 days)
 

Hello!

Hoping for some help to finalize our itinerary before we start booking hotels. We are a couple from Canada in our mid-twenties traveling to Japan for the first time.
Here's what we've got so far (bold indicates where we're staying the night):

Tues September 11: Arrive in Tokyo at 6:30 PM
Wed September 12: Tokyo
Thurs September 13: Tokyo (day trip to Nikko)
Fri September 14: Tokyo
Sat September 15: Tokyo --> Kyoto
​​​​​​​Sun September 16: Kyoto (day trip to Himeji)
Mon September 17: Kyoto
​​​​​​​Tues September 18: Kyoto (day trip to Osaka)
Wed September 19: Kyoto (day trip to Nara)
Thurs ​​​​​​​September 20: Kyoto --> Koya-San
Fri September 21: Koya-San --> Hiroshima
Sat September 22: Hiroshima (day trip to Miyajima)
Sun September 23: Hiroshima --> Hakone
Mon September 24: Hakone --> ??
Tues September 25: ??
Wed September 26: ?? --> Tokyo
Thurs September 27: Depart Tokyo at 9:50PM

I *just* realized that the hand-made calendar I made was missing a day, so now I have an extra day at the end I don't know what to do with. I was really hoping to stay somewhere on the Izu Peninsula for a night, like Shimoda, but it appears that the train ride to and from the area is several hours. Would it be worth it?
If not, where should I spend that extra night/add an extra night somewhere earlier in the trip?
Any advice would be very welcome. Thank you!

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I would add another night in Hiroshima, rather than adding another city. We spent three nights there, which included a FULL day at the Peace Museum (we took a lunch break), and another full day for Miyajima. The Peace Museum is fascinating, and they have video recordings of survivors, which we found very sad but interesting. In fact, I just finished reading "Hiroshima" by John Hersey, whose insights will undoubtedly enhance your visit to the city. On a lighter note, you could possibly catch a baseball game while you are there.

Looking at your itinerary, you have six different hotel cities (counting Tokyo twice), which to me, is quite a bit for seventeen nights. Although trains are pleasant and efficient, it still takes time to get form place to place.

If you add a night to Hiroshima, you could do Himeji as a day trip from there - it's likely easier to do than from Kyoto because you won't have to switch trains at Shin-Osaka (check Hyperdia - you can catch the Sakura shinkansen from Hiroshima to Himeji, if you're on a JR pass you cannot use Nozomi or Mizuno shinkansen).

You should add a night or two to Kyoto. You won't run out of stuff.

Get the two-week JR passes and start them on 9-14 when you arrive in Japan.

If it was me - and it isn't - I'd consolidate all of my Tokyo time into one stay, reducing your changes of hotels by one. So I would go from Narita to Kyoto on day 1. I also wouldn't add another stop, just add those "found" days to the places you have already decided to visit.

Right now , you only show one full day in Kyoto - not nearly enough! Kyoto can soak up huge amounts of time, there is so much to see/do/experience. If you had no day trips from Kyoto, those four full days win Kyoto might be enough. We had 5 full days in Kyoto and would have enjoyed even more time there (we never got to Nara).

While it probably seems to you like you aren't going that many places, I think you do have too much on your schedule, mostly because you have crammed your Kyoto time full of day trips.

+1

The day trips you have planned from Kyoto (Himeji, Osaka, Nara) are worthwhile (and I wouldn't suggest dropping any of them) but, for my taste, you don't have nearly enough time in Kyoto itself. We've been to Kyoto .... I think it's five times now. We were there for a couple of weeks last April/May, again last October for 10+ days and we'll be there again in October this year. Although it's easy to get "templed out", it never tires for us. For us, it's the gardens rather than the temples themselves (and we're not gardeners but there's something sublime about Japanese gardens). Kyoto (supposedly) has 400+ shrines and 1,700+ temples, most of which probably have a garden of some sort. Go to Arashiyama and visit the Bamboo Grove, Tenryu-ji and Okochi Sanso. On the way back, go to Nijo Castle. Walk through the Imperial Palace grounds. Visit the Nishiki Market. Head west again to Kinkaku-ji, Ryoan-ji and the temples at Daitoku-ji. Go east to Higashiyama and its many temples. Walk the Path of Philosophy up to Gingaku-ji. Wander the back streets of Kyoto (with a phone, and maps and a GPS function on your phone, you can't get lost). Work your way through the ramen shops on the 10th floor of Kyoto Station. On the way to Nara (to see the Big Buddha and to feed the deer...), stop and visit Fushimi-Inari. Visit the railway museum. There are endless things to do, places to go.... The https://www.insidekyoto.com site has lots of information.

As Kathie has suggested, I would think about changing the sequence of your trip, perhaps to make Kyoto the last stop. You can easily make it back in a few hours from Kyoto to Narita/Haneda so no need to head back to Tokyo any earlier than the day you fly out.

Thank you all so much!

It makes much more sense to consolidate all the Tokyo time. I guess I was just nervous to take the train to Tokyo from another city on the last day, with the small chance that something goes wrong and we miss our flight. I also thought it would be awkward to drag along our luggage (although we are just bringing carry-ons) in Tokyo if we arrive there too early before our flight departs.
We are flying into and out of Haneda by the way.
If we arrive at Haneda at 6:30 PM on our first day, would it be pretty reasonable to carry on straight to Kyoto from there?

Here's the next draft of my itinerary:

Tues September 11: Arrive at Haneda Airport at 6:30 PM --> train to Kyoto
Wed September 12: Kyoto
Thurs September 13: Kyoto (day trip to Osaka)
Fri September 14: Kyoto
Sat September 15: Kyoto (day trip to Nara)
Sun September 16: Kyoto
Mon September 17: Kyoto --> Koya-San
​​​​​​​Tues September 18: Koya-San --> Hiroshima (if we leave early in the morning can we do the museum this day? Although I believe traveling to and from Koya-San takes a few hours, with no JR pass option?)
Wed September 19: Hiroshima (day trip to Miyajima)
Thurs ​​​​​​​September 20: Hiroshima (day trip to Himeji?)
Fri September 21: Hiroshima --> Hakone
Sat September 22: Hakone --> Tokyo
Sun September 23: Tokyo
Mon September 24: Tokyo
Tues September 25: Tokyo (day trip to Nikko)
Wed September 26: Tokyo (or do an extra day in Kyoto instead?)
Thurs September 27: Depart Tokyo at 9:50PM

What do you think of this? I added an extra day in Kyoto and Hiroshima, and changed the day trip to Himeji from Hiroshima instead of Kyoto. Although, I wouldn't mind having a whole day in Hiroshima like CaliforniaLady suggested. Should I do the day trip to Himeji from Kyoto or Hiroshima with this schedule?
Or, should I drop one of the days in Tokyo and add one to Kyoto instead? Right now I pretty much have 6-ish days in Tokyo (with one day trip) versus 5 days in Kyoto with 2 day trips.

Also, I'm finding it a bit overwhelming with the trains. I am using hyperdia.com, but it seems some cities have multiple stations, etc. Any tips? Should I set my itinerary first and then worry about trains, or plan out every single route first?

Thanks again so much for all you input - much appreciated!

IMHO to preface....
I would suggest cutting either Hakone or Koya adding more time to Kyoto and Tokyo
17 days counting arrival and departure is more like 14/15 days actual. .
Quite true you can get to Narita from Kyoto in good time.
With all your daytrips you are not leaving enough time to enjoy Tokyo or Kyoto in a leisurely fashion.
Hakone, Koya, Osaka, Himeji, Hiroshima, Miyajima are all worthy destinations but as I said IMHO for a first time trip I would suggest a less stressful itinerary and plan on returnining for more in depth exploration.
Whatever you decide have a good time

There is obviously always a chance that something goes wrong - perhaps there will be an earthquake and all bets are off - who knows! - but train travel in Japan is unbelievably, amazingly efficient. This is a country where they publicly apologise because a train left 40 seconds early....

I would say no. It can be done but the odds are against you. From Haneda, you need to get to Shinagawa to get the Shinkansen. The last Shinkansen to Kyoto leaves at 8.10 pm, so with a 6.30 pm arrival at Haneda it's possible but I wouldn't try it. Even with just carry on, you have to be on-time, off the plane promptly, through immigration and customs, find the JR ticket office to exchange your JR pass, get the (non-JR) train to Shinagawa or (using the JR pass) take the monorail to Hammamatuscho and the JR Yamanote line to Shinagawa. If the stars are aligned, it's possible but ...

Whatever the schedule, I would do it from Kyoto.

Hyperdia is outstanding but it can be a bit finicky. You have to spell the station exactly the way it wants it or it will say "Route not found". As you start to type a station name, it will give you a drop down list so try and pick from that if you can. Sometimes spacing and/or hyphens aren't the way you might expect (so, e.g., if you're going to the Bamboo Grove and you want the train to Saga Arashiyama [or is that Saga-Arashiyama?], Hyperdia will want Sagaarashiyama, with no space or hyphen).

Yes, there can be multiple stations with similar names and/or close to each other - you just have to be sensitive to that. The Shinkansen stops at Shin-Osaka, which is a bit north of Osaka and a different station. If you ask Hyperdia for Shinagawa -- Osaka, you'll see it sends you on the Shinkansen to Shin-Osaka and then on a local JR train to Osaka.

Hyperdia will tell you the fare for every route. There will always be two elements - a "fare" and a "seat reservation" fee. If the seat reservation fee = ¥0, then no reservation is required but if there's a seat reservation fee, then you need a reservation (which is free on JR trains, if you're using a JR Pass). The Shinkansen has several cars that are "unreserved" -- for which you -- theoretically -- still need a reservation, except if you have a JR Pass. That is, there will a 'reserved seat" fee and an "unreserved seat" fee, the latter of which is cheaper. If you're buying a Shinkansen ticket (i.e., not using a JR Pass) you can opt for either. If you're using a JR Pass on a Shinkansen, you can either get a 'reserved" seat, which the ticket office will give you for free (i.e., the seat fee is covered by the JR Pass) or you can just get on one of the unreserved cars (without going to the ticket office for a reservation) and take your chances that there's an available seat (or else you stand...). For non-Shinkansen trains, if there's a seat reservation fee, that means a reservation is required .... unless there is also an "unreserved seat" fee (like a Shinkansen), which implies the train has "unreserved" carriages. If there's only a 'seat reservation' fee, that implies the train doesn't have unreserved seats and you'd need to get a (free) reservation.

Train travel isn't particularly cheap but it is amazingly efficient and Hyperdia makes it easy to figure out how to get from A to B (subject to the issues above). In particular, the fares are the same, no matter when you buy the ticket (though that's not particularly relevant if you're using a JR Pass). Get a Suica card (or a Pasmo or ICOCA card) - a prepaid travel card - to use for all non-JR trains, subways and buses. They can also be used to pay for purchases at 7-Eleven, cafes etc. etc. and can be easily topped up at any station ticket machine (and the trick there is to first find the button that says "English"....)

"I guess I was just nervous to take the train to Tokyo from another city on the last day, with the small chance that something goes wrong and we miss our flight."

Done this twice. Trains were completely on schedule. More reliable than atomic clock.

A couple of further thoughts.... As Kathie has already suggested, I would try to minimise the number of hotel locations/changes - it just makes life easier. Most of the places you want to go can be done as day trips from either Tokyo or Kyoto.

In regards to how much time to spend in Tokyo versus Kyoto, this article - https://trulytokyo.com/tokyo-or-kyot...uld-you-visit/ - has a comparison of the two which I think provides a fair assessment of their different characteristics. Obviously only you can decide what appeals more to you....

As noted earlier, I don't think it's realistic to try and make it to Kyoto the day you arrive. Consequently, I would suggest flipping the agenda around by starting in Tokyo and ending in Kyoto. As for getting the train back to Tokyo the day you fly out, as BigRuss succinctly observed, Japanese trains are more reliable than the atomic clock...

Although I haven't done it, many people do Hakone as a day trip from Tokyo. One advantage about doing day trips from Tokyo (or Kyoto) is it gives you some flexibility to decide which day to do them and you can change your schedule as circumstances and the weather dictate. For Hakone, my daughter was there two weeks ago (en route from Tokyo to Kyoto); the day they had scheduled to be there turned out to be overcast, so much so that there was no sign of Mt. Fuji and the boat trip (the final part of the Hakone Loop) was cancelled. In another forum, somebody who was there the day after her commented how great the weather was and how fabulous was the view of Mt. Fuji .... so far, I haven't had the heart to tell her... If you do it as a day trip, you can stay flexible and pick whichever day looks like it's going to have the best weather.

From Kyoto, it's easy to do day trips to Himeji, Nara and Osaka. You can also do Hiroshima as a day trip. We did that last year, though we didn't go to Miyajima. Including Miyajima will make for a long day but it can be done. From Kyoto, there are a couple of Shinkansens in the morning that don't require a change at Shin-Osaka, the optimum one leaving Kyoto at 7.20 am, arriving in Hiroshima at 9.05. The last one back is around 7.50 pm (changing in Shin-Osaka). If the goal is to visit the Atomic Dome and the Peace Park in Hiroshima and then to visit Miyajima, you should be able to do that in the day (though it won't leave much time for anything else). The link at the bottom of this page will show you the tide times at Miyajima - https://www.japan-guide.com/e/e3450.html. I think getting there involves a 25 minute train ride from Hiroshima station and then a 10 minute ferry ride, so depending on the tide times, you may want to go there first and then come back to the Atomic Dome etc. in the afternoon.

I assume you're planning on getting a 14 day JR pass? Given that you have a total of 17 days, you obviously get caught short. However, if you flip Kyoto and Tokyo, you don't need to activate the pass until Friday, September 14 (day trip to Nikko?) and it will then last until your final day getting back to Tokyo and the airport. If you do that, get a Suica card each when you arrive and use that to get the monorail and JR Yamanote line to wherever you're staying in Tokyo. A JR pass is of limited use around Tokyo (except of course for day trips) so not having it for the first few days is not really an issue.

Again, thank you all!! Feeling a little overwhelmed here. It's been awhile since we've planned a major trip!
I understand the recommendation to cut down the amount of hotels... however, I was really hoping to stay a night each at an onsen ryokan in Hakone (but totally understand the benefit of doing a day trip to ensure a clear day to see Mt Fuji too...), and at a temple in Koya-San. Has anyone done both and preferred one over the other? Would staying an an onsen ryokan in Kyoto for a night be just as nice as Hakone (I think there are a couple in Kyoto)?

Thank you ttj for the website outlining Tokyo vs Kyoto... our personalities are definitely more suited to Kyoto.

Let's switch things around again and start in Tokyo... I also switched out Hiroshima for a day trip instead).

Tues September 11: Arrive in Tokyo/Haneda Airport at 6:30 PM
Wed September 12: Tokyo
Thurs September 13: Tokyo
Fri September 14: Tokyo (day trip to Hakone* or Nikko depending on weather; initiate 14 day JR pass)
Sat September 15: Tokyo
Sun September 16: Tokyo (day trip to Nikko or Hakone*)
Mon September 17: Tokyo --> Koya-San
Tues September 18: Koya-San --> Kyoto
Wed September 19: Kyoto
Thurs September 20: Kyoto (day trip to Nara)
Fri September 21: Kyoto (day trip to Osaka)
Sat September 22: Kyoto
Sun September 23: Kyoto (day trip to Hiroshima +/- Miyajima)
Mon September 24: Kyoto
Tues September 25: Kyoto (day trip to Himeji)
Wed September 26: Kyoto *stay in an onsen ryokan this night in lieu of cutting out a night in Hakone? Or travel from Kyoto to Hakone instead this day, and travel from Hakone to airport tomorrow? (if this is the case, I may cut one day from Tokyo and add one to Kyoto)
Thurs September 27: Kyoto (or Hakone?) --> depart Tokyo/Haneda Airport at 9:50PM

Thanks again!!

I would really re-think Koya-San. It seems very much out of the way. If it is Koya-San in Wakayama Prefecture, look at the time it will take to get there. Yes, it sounds wonderful to stay in a temple, but perhaps look for other towns you might be able to do this. I also suggest you look at festivals occurring in the cities you plan to visit scheduled in September. They are wonderful to experience and the locals are very welcoming, especially in the smaller cities.

I would also recommend you start watching NHK programs with a wonderful diverse schedule of shows on cable or by streaming. We took our first trip to Japan for 30 days in the spring to many of the areas you are planning to visit and we learned so much about the culture, the food, the history and how to comport ourselves when in a restaurant or store. Tokyo 2020 is our current favorite show as we just can't stop watching while we plan our 2nd trip to Japan next year.

Highly recommend the JR pass, Nikko and Nara. Hiroshima + Miyajima can be done in a day, especially if you take the Aqua Net ferry between the Peace Park and Miyajima.
Check the tide schedule - we were surprised by the low tides at the Peace Park thus preventing us from taking this ferry.

Looking forward to your future posts. Here to help!

More random thoughts.....

You (presumably) haven't done anything yet about a JR Pass, as you have to exchange the JR voucher you receive (in Canada) for the actual pass (in Japan) within 3 months of the voucher being issued (so at least another 10 days or so before you can purchase). Given the amount of train travel/day trips you're proposing, the pass will certainly be cheaper than individual tickets (though you can confirm that by pricing all the train trips you propose using the fares shown in Hyperdia (including seat reservation fees) and comparing that with the cost of the Pass. The only negative with the Pass is that you can't use the faster Nozomi Shinkansens (faster because they make fewer stops) so remember to turn the Nozomi box "off" when you're searching in Hyperdia. As for the Green Car Pass (first/business class) versus the Regular Pass, we've always just used the Regular Pass (or tickets). In the regular Shinkansen cars, the seating is 3 x 2, in Green Car it's 2 x 2. The Green Car seats have a few extras (like footrests) and they're obviously slightly more spacious but we've always found the Regular seats perfectly adequate. They're comparable to an airline economy seat but with much better leg room (in part due to the fact that the seats rotate, so you'll always find yourself facing forward on a Shinkansen - the train doesn't rotate but the seats do...). Non-Shinkansen JR trains may not have Green Car carriages so, for them, the Green Car Pass is of no advantage. Obviously, the JR Pass only works on JR trains and not on the subway, buses or non-JR (private) railways (of which there are quite a few). Whether you stick to a Regular JR Pass or pay the extra for a Green Car pass is obviously a matter of personal preference.

For the subway, buses, non-JR trains etc, just get a Suica (prepaid) card and top-up as necessary. It makes travelling far, far easier - no messing about trying to figure out what subway ticket to buy or fiddling for change to buy it with - just swipe the card on the gate and off you go. There are various "flavours" of these cards - Suica is issued by JR in Tokyo, Pasmo is issued by the non-JR (private) rail operators in Tokyo, ICOCA is the flavour in Osaka, and so on. However, all these cards are now inter-operable so a Suica card will work in all the places you're going. See here -- https://www.japan-guide.com/e/e2359_003.html. Note that if you use the Suica on a non-JR train that has a seat fee, the Suica will only pay the base fare and you'll need to go to a ticket machine/ticket office to pay the seat fee ..... but as all your travel will probably be on JR trains (other than local travel, subways, buses etc.) that should be a non-issue.

When you arrive, get a Suica card each (though check to see if your local JTB office (Japan Tourist Board) or whoever you get the JR Pass voucher from can sell you them before you go). Use that for the monorail from Haneda and other travel for the first few days before the JR Pass is active. You can exchange the JR Pass voucher for the actual pass at major ticket offices (there'll be a list in the material you get with the voucher). I would do that on the Wednesday after you arrive; you just need the voucher and your passport with the "temporary visitor" stamp they'll put in it at immigration when you arrive. Make sure you specify September 14 as the start date (though they'll ask you that). The actual pass will show the date it expires - so make sure that's September 27!

Depending on where you're staying, Shinjuku Station may be the easiest place to do it. If you do go to Shinjuku, don't end up like this chap .... https://www.therisingwasabi.com/man-...tion-exit-27k/ .... :-)

Any and all questions about the JR Pass, Suica etc, please just ask.

Re the recommendation above to 'rethink Koyasan' and consider spending the night in a temple elsewhere: yes, time is tight but a night on Koyasan is more than spending the night in a temple. Isn't it a sacred mountain, so more of a pilgrimage? If it is important to the OP and if h/she is up for a hard travel day, it's probably an irreplaceable destination.

How much you enjoy your stay in Koya-san depends very much on which temple you pick. I did enjoy getting there, the train ride was scenic, but my temple was disappointing and I did not get to visit the cemetery at dusk.

A nice ryokan stay with onsen and a night in Koyasan are very different experiences. I've done both but didn't get to Koyasan until my third trip to Japan (just returned on Monday). I thought the temple stay would be a defining part of the experience but it wasn't, in that the accommodation and meals were like being in a simple ryokan. The highlights (for me) were the 45 minute morning service and our 3 walks through the cemetery, afternoon, dusk/night and morning. IMHO, a better choice for a first trip to Japan would be a ryokan in an onsen town where the travel to and from is not so difficult (3 or 4 connections each way depending on where you are coming from and going to). I am very glad we went to Koyasan but there are a lot of tourists there now - so it was less "spiritual" than I thought it would be. But Okunoin was pretty amazing.

Koya-San and Hakone

I must admit, I had to look up Koya-San to see where it was, so not being at all familiar with it, had refrained from commenting before now until I figured out whether there was anything useful I could say (which there probably isn't...). It does seem hard to get to - 2.5 hours from Kyoto and three changes of train, though I applaud your desire to go there. Others have now been able to comment on Koya-San, although their comments don't seem overwhelmingly positive. The only suggestion I could make would be to do it on your last full day (September 26) - head there early in the morning from Kyoto, stay overnight and then head to Tokyo the following day to get the flight home.

As for Hakone, forget doing it as a day trip - do it on the way to Kyoto so you can stay in a ryokan. You just have to hope the weather gods are on your side! There are various ways of getting there but the Shinkansen (either Hikari or Kodama) to Odawara is the quickest and easiest - 27 minutes from Shinagawa, with one stop at Yokohama. Once there, get the Hakone Free Pass and do the Round Course. Next day, back to Odawara at some point and get the Shinkansen to Kyoto. When you get to Odawara, I believe there's a luggage service that will take care of getting your bags to wherever you are staying.

Hotels - not sure where you've got to with accomodation? In Tokyo, Shinjuku is a popular area to stay though others seem to like Ueno or Asakusa. Last trip, we stayed in Tokyo for a few days and stayed at an AirBnB in Shinjuku. On her last couple of trips, my daughter has stayed at the Hotel Gracery Shinjuku and she seems to like it. Japanese hotel rooms (and AirBnB apartments) tend to be much smaller than you may be used to. We tend towards the "cheap and cheerful" end of the spectrum rather than the Ritz Carlton/Mandarin Oriental end, as hotel facilities and the size of the room are of little interest to us - we're there to see the sights, not spend time in the hotel or the room.

In Kyoto, our last couple of stays have been AirBnB and our preference has always been to be close to Kyoto Station. Most days, activities seem to start and end at the Station (particularly if you're doing days trips to Himeji, Hiroshima, Nara, Osaka etc.) so being a few minutes walk from the Station has always been a plus. Kyoto Station, with its soaring atrium, is almost a destination in itself, with lots of restaurants in and around (or underneath) the Station. Don't miss the ramen restaurants on the 10th floor - Kyoto Ramen Koji

You all are awesome! Thanks again for all the advice regarding trains/passes and Koya-San opinions. No, we haven't looked into hotels yet. We're willing to splurge for 1 night or so, but otherwise prefer decently priced places in convenient locations.

I think I will have to look more in depth into Koya-San. It wasn't a "must-see" for me; to be honest most of my Japan research thus far has been from my Lonely Planet guides, but I will take some time this weekend to sit down and read more reviews. I was hoping staying at a temple would be a neat spiritual experience (although I am more of a spiritual person than my partner so he may not enjoy Koya-San as much anyway).

I will also have to look into festivals and such. We want to attend a Sumo tournament and I think there is one in September.

I think I'll switch out Koya-San for Hakone now...

Tues September 11: Arrive in Tokyo/Haneda Airport at 6:30 PM
Wed September 12: Tokyo
Thurs September 13: Tokyo
Fri September 14: Tokyo (day trip to Nikko; initiate 14 day JR pass)
Sat September 15: Tokyo
Sun September 16: Tokyo
Mon September 17: Tokyo --> Hakone (ryokan with onsen)
Tues September 18: Hakone --> Kyoto
Wed September 19: Kyoto
Thurs September 20: Kyoto (day trip to Nara)
Fri September 21: Kyoto (day trip to Osaka)
Sat September 22: Kyoto
Sun September 23: Kyoto (day trip to Hiroshima + Miyajima)
Mon September 24: Kyoto
Tues September 25: Kyoto (day trip to Himeji)
Wed September 26: Kyoto
Thurs September 27: Kyoto --> depart Tokyo/Haneda Airport at 9:50PM

I liked your original plan better. Changing hotels is just not a big deal if you travel light. Starting and ending in Tokyo is just fine and easy. Your first night you can just stay in Shinagawa and just head south from there the next day. No need to rush to Kyoto the first night. You could fly to Hiroshima from Haneda.

Hiroshima and Miyajima really deserve more than a day trip from Kyoto. I don't see the point of dealing with Kyoto traffic (depending on where you stay) to from the JR station, the train rides. No reason to pay a Kyoto hotel rate when you can probably get better for less in Hiroshima. So many ways to do it. Like, leave your bags at your Kyoto hotel and take just what you need for one night.

Chiming in a bit late here, but FWIW:

I thought Koya-san magnificent. I stayed at Shojoshin-in, which still gets great reviews. My time at the temple, and at various sites in Koya-san, was among the highlights of a highlight-filled trip.

I must admit that I don't understand why so many travelers think one-night stays at hotels are unbearable, particularly in a country like Japan with excellent luggage forwarding options. (Luggage-forwarding is called takuhaibin; here's the info:
http://www.japan-guide.com/e/e2278.html)

Like mrwunrfl, I think Hiroshima and Miyajima deserve more than a day trip. I was glad to spend a night on Miyajima, and would have happily spent a second night there if doing so would have made sense for my itinerary.

Whatever you decide, I'm sure it will be a great trip. :)

I didn't realize it was possible to leave bags at a hotel and have them hold the bags for a night?
In that case...

Tues September 11: Arrive in Tokyo/Haneda Airport at 6:30 PM
Wed September 12: Tokyo
Thurs September 13: Tokyo
Fri September 14: Tokyo (day trip to Nikko; initiate 14 day JR pass)
Sat September 15: Tokyo
Sun September 16: Tokyo
Mon September 17: Tokyo --> Hakone (splurge on a ryokan with onsen)
Tues September 18: Hakone -->Kyoto
Wed September 19: Kyoto
Thurs September 20: Kyoto (day trip to Nara)
Fri September 21: Kyoto (day trip to Osaka)
Sat September 22: Kyoto
Sun September 23: Kyoto --> keep bags at Kyoto hotel and take small backpack to Hiroshima early in morning to spend whole day at the Peace park, overnight in Hiroshima
Mon September 24: ferry to Miyajima in morning, then train back to Kyoto
Tues September 25: Kyoto (day trip to Himeji)
Wed September 26: Kyoto
Thurs September 27: Kyoto --> depart Tokyo/Haneda Airport at 9:50PM

Still considering exchanging a day in Tokyo for Kyoto.

Some of us prefer not changing hotels unless we have to, with its attendant packing up / checking out / checking in / oh, you mean we can't check in yet / what do we do with our bags?... For us, it has nothing to do with luggage as we travel light (with carry-on only) and changing hotels is certainly not unbearable. However, Japan is perhaps unique in that its trains are so frequent and so efficient that it's practical to do day trips from a selected base, so that changing hotels simply becomes unnecessary. As for time on trains, Hiroshima is only 1 hr 45 mins from Kyoto and sometimes it's nice to just sit back and watch the world go by, catch up on writing the diary etc.

I don't disagree that Hiroshima and Miyajima deserve more than a day trip..... but then so do a lot of places. If you're on your first trip to Japan and you have 15 days to play with, and (potentially) so many other places to go and things to do, I doubt many people would choose to spend two days at Hiroshima and Miyajima. Conventional wisdom would have you go to Tokyo and Kyoto, with perhaps a few day trips thrown in. I haven't been to Miyajima but I assume that most people go primarily to see the torii gate, either at high tide, low tide or both and/or at night. I agree that to do that properly, you need a couple of days but would you do that (at the expense of other places) on a first visit to Japan? If you want to see a big orange torii gate, go to Heian-jingu in Kyoto (ok, it doesn't appear to float on the water at high tide, more like sit on the concrete, but it's an impressive gate ....).

Perhaps there are other things to do in Hiroshima and Miyajima that make a two+ day stay compelling for a first time visitor? I know that CaliforniaLady said they spent an entire day at the Peace Park though, personally, I'm not sure what you would do there to occupy an entire day. For our part, we visited the A-Bomb Dome, toured the Peace Museum (including time spent watching the video testimony of survivors), toured the Peace Park, including the Children's Peace Memorial and the Peace Bell -- had we stayed longer, I don't know what we would have done and I certainly don't feel like we short-changed the experience in any way. After that visit, we took the tram to the Shinikkien Gardens. After touring the gardens, we walked back to the station, had a late lunch and then caught the train back to Kyoto (in time for tea...)

To each his/her own! For me, the time it takes to backtrack is wasted time, and I don't like to waste my precious travel time. Obviously, others feel differently. And yes, there's more -- much more -- to Miyajima than Itsukushima. I firmly believe that travelers should plan their time to suit their personal interests, something that requires research and not simply relying on the advice of people who didn't visit places they are considering. JMO.

Good itinerary. You should consider spending the night of the 24th on Miyajima and then visit Himeji on the 25th on the way back to Kyoto. You will be able to use a coin locker for that backpack at Hiroshima station and at Himeji.

You could move the Hakone stay to the end. You could have an onsen soak before you head to the airport.

>> oh, you mean we can't check in yet / what do we do with our bags?.
you leave them with the front desk or bell captain
[or, it could be more convenient to toss your bag in a locker at the station, go out and about, then fetch your bag and check in later when you are ready to use your room]