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]