Even though there are many (not all) here, myself included, who have expressed preference for Kyoto over Tokyo, there is still plenty to see and do in Tokyo for several days, especially when including day trips.

We enjoyed visiting Kamakura on our last trip, you also have Nikko (which also works well as an overnight, but many do it as a day trip happily).

Btw, if you are really into cooking, you may enjoy half a day browsing in Kappabashi Dori, though if you aren't a kitchenware geek, may want to skip it.

In terms of the questions about Osaka, I feel there is less to see and do there though it does depend on your interests. I enjoyed the cup noodle museum when I first went (though there's another larger one in Yokahama, near Tokyo). A friend says the aquarium is good. I thought the small food market there very enjoyable to browse, far less crowded than Nishiki though Nishiki is incredible. I didn't rate the knife museum in Sakai but there was a pleasant temple on the way out to it. I would say that yes there are some great Osaka foods to try but you could easily do an afternoon and evening visit from Kyoto rather than overnight, that's what I would recommend anyway.

Takayama, you can do two nights there if you give a good part of arrival day and departure day to it too, but I wouldn't try and also cram in S-Go into the same two day visit. For Kanazawa, it depends on what you want to see - we did 4 nights but could have managed happily with 3. We loved the famous gardens, not so much the reconstructed castle. Adored the food market there, not so much the tea districts which we felt were small and less charming in comparison with Kyoto and Takayama's historic districts. The samurai district was interesting to us. We didn't bother with the modern art museum other than briefly enjoying some of the outdoor pieces. So it all depends on what you want to see.

>>Planning our mid-November trip ...

Oh! That is a great time to go to Japan and good for all your stops,

Kanazawa should be warmer but wetter than Takayama. Kanazawa temps 10-12F higher, precip 10" vs 2".

Takayama will be on its way to winter with near freezing overnight temps.

Kanazawa might still have some fall color. Also, Kanazawa has a practice called yukizuri where they tie up tree branches to protect them from snow. It was cool/charming to see. It is a symbol of Kanazawa (my Starbucks cup has images of the four seasons in Kanazawa and the autumn one features leaves and yukizuri trees)

I would (and did) choose Kanazawa over Takayama at that time. It didn't rain.

Here is info about yukizuri:
http://www.kanazawa-tourism.com/eng/event/event3.php

and here, along with a nice fall colors photo in Kenrokuen
http://www.japan-guide.com/e/e4200.html

... and it would be easy to visit Shirakawago from Kanazawa. Shirakwago might be less photogenic then than at other times of the year (my guess is that it would be too early for snow).

>>Takayama will be on its way to winter with near freezing overnight temps

I meant to add "but less chance of rain" to that. The weather numbers I gave above are monthly averages from weatherbase.

November is a wonderful month to visit Japan - not just climate-wise but for observance of Shichi Go San when girls aged 7 and 3 and boys aged 5 are taken to the shrines in traditional dress. Mothers and grandmothers usually wear kimono as well. Not so great though for momiji (maple viewing) crowds.

I am one of the few here who prefers Tokyo over Kyoto, but then I have a strong aversion to crowds. I spent five days in Kyoto at end-March this year and couldn't believe the people jams midweek in Arashiyama. The Bamboo Path was a nightmare. To be fair, I suspect the crowds were in hopes of hanami which was late this year.

To categorise Tokyo as simply 'ultra urban culture' is to misunderstand the many levels of this city. The secret is not to be intimidated by the sprawling metropolis but to approach it at neighbourhood level where one finds the 'traditional' (though never sure what is meant by that). And because it is so big and offers so much - it is easy to beat the crowds, a trick I have not yet discovered in Kyoto.

Tokyo vs Kyoto as modern vs traditional is a false dichotomy. Take the Asukura Choso Museum in Tokyo: behind the modern exterior is one of the most beautiful traditional Japanese residences. And because it is so quiet, you can actually sit awhile,looking out at the amazing inner courtyard water garden, smelling the fresh tatami (and not the feet of fellow visitors). .

Osaka as foodie destination is overhyped in my opinion but then okonomiyaki is one of the few Japanese meals I am not crazy about.
If you are foodies - might be worth looking into booking at one of the one-starred Michelin soba, tonkatsu or yakitori places in Tokyo - not expensive. Do that two months in advance if possible.

"To categorise Tokyo as simply 'ultra urban culture' is to misunderstand the many levels of this city. The secret is not to be intimidated by the sprawling metropolis but to approach it at neighbourhood level where one finds the 'traditional' (though never sure what is meant by that). And because it is so big and offers so much - it is easy to beat the crowds, a trick I have not yet discovered in Kyoto.

Tokyo vs Kyoto as modern vs traditional is a false dichotomy. Take the Asukura Choso Museum in Tokyo: behind the modern exterior is one of the most beautiful traditional Japanese residences. And because it is so quiet, you can actually sit awhile,looking out at the amazing inner courtyard water garden, smelling the fresh tatami (and not the feet of fellow visitors)."

Boveney, I would love to pick your brains further on the other facets of Tokyo before my next trip.

I think when people summarise Tokyo as modern, Kyoto as traditional, they are not suggesting that either city only offers that one aspect, only that it's much easier to find those aspects of Japan in the cities, respectively. But of course, Kyoto has much of modern Japan and Tokyo has traditional to offer too.

I would like to explore more of neighbourhood Tokyo next time, rather than the usual suspects when it comes to districts, though they suited me fine for my first 3 trips. Will definitely remember ask for your input!

just for the sake of this interesting discussion ...

>>Tokyo vs Kyoto as modern vs traditional is a false dichotomy.

You say that yet you are "never sure what is meant by" traditional. It is not a dichotomy, really, it is a matter of balance, as Kavey suggested.

Traditional Japan can be found everywhere in Japan, both modern traditions and ancient ones. Halloween, Christmas, sake brewing, gassho zukuri.

I think that "traditional Japan" is often used as shorthand for cultural heritage as defined this way

Tangible Cultural Heritage. ... Cultural heritage is the legacy of physical artefacts and intangible attributes of a group or society that are inherited from past generations, maintained in the present and bestowed for the benefit of future generations.

Kyoto really is the heart of the Japanese cultural heritage. Takayama and Kanazawa both have cultural heritage sites, but it is interesting that both (like other places in Japan) are referred to as "little Kyoto".

Kyoto is a modern city, so are Osaka and Fukuoka, but if you want to get to the heart of ultra-modern Japan you go to Tokyo.

See, I think if you want to get to the heart of Japan (modern and traditional both, the whole package), you can't shortchange Tokyo (which posters here often advise) . I suspect 'traditional' is often used in discussions here as a shorthand for 'old' - which is something the Japanese themselves don't put all that much stock by. Just have to pick up on your mention of Halloween as a 'new tradition' - ouch. This is one that hurts. When we lived here thirty years ago the autumn cards that were exchanged bore the seven seasonal flower motifs. We moved back four years ago to find they are now all of jack o lanterns, witches and cats! But that aside, in Tokyo one finds the ancient traditions flourishing in modern interpretations (art, design, food, architecture etc) - I'd argue that is the real value of 'cultural heritage'.

What day in November is day 1? You don't want to miss shichi-go-san at Meiji Jingu. The day is the 15th. The Sundays before and after would be good.

I've enjoyed it twice on Sundays when the 15th was a weekday (like this year). In addition to the children, there were Shinto wedding parties (I believe they enjoyed the attention they got from others).

Although technically Shichi Go San is 15 November, it doesn't matter - it happens throughout November though obviously weekends will be most popular.

Thank you everyone for all of your input. I have taken your feedback and reconfigured the itinerary:

5 nights in Tokyo

2 nights in Takayama (possibly visit Shirakawago?)

1 night in Koyasan

5 nights in Kyoto (day trip to Nara)

1 night in Hakone

2 nights in Tokyo

There is a pretty clear issue with getting from Takayama to Koyasan that I need to figure out. Should I just not do Koyasan and stay a night in Nara instead?

I feel like Hakone can be our opportunity to try the onsen and also, if lucky, get a great glance at Mt. Fuji.

How many Ryokan would you suggest we try? Maybe 1 or 2? If so, where are the best destinations to do so?

Thank you!!

That Takayama - Koyasan leg is a no-go for me.

A few options in no particular order:

-- Add a night to Takayama. With just two nights you would not have enough time for S-go, but you could visit Hida No Sato. With three nights you could visit S-go and have more time for Takayama.

There is an onsen at the Green Hotel in Takayama that is open to the public (am not recommending the Green as a place to stay).

With 3 nights, you could split your stay in Takayama to 2 nights hotel (Best Western) and 1 night in a ryokan. I stayed at Sumiyoshi Ryokan and thought it was ok, others loved it.

-- Split your stay in Kyoto. Go Takayama to Kyoto for 2 or 3 nights then an overnight trip to Koyasan and back to Kyoto. Nara could be part of that side-trip, either as another overnight stay or on the way back from Koyasan to Kyoto.

I haven't commented on the length of your Tokyo stay. You had four full days with daytrips to Kamakura & Nikko leaving two days for Tokyo itself. And it turned out you had a Disney plan for that last full day. So I could see how that would work out.

But now is the time to figure out your Tokyo time especially if you want to keep Koyasan. You could cut Nikko or Kamakura or both.

Kamakura, for example, sounds like it is a "seems interesting" stop. Other people have a definite interest and plan for visiting there. After looking into it more, I just decided to swing by Kamakura to visit the Daibutsu (nice with the late fall colors) on the way from Hakone to Tokyo. I still haven't been to Nikko.

oh, and Hakone would be a good place to find an onsen ryokan. You could move that stop to earlier, of course.

I would not travel Koyasan to Hakone for a 1-night stay. But, Koyasan to Tokyo is a bit easier and quicker (because of the greater availability of the faster shinkansen that don't stop at Odawara). I might bite that bullet given that the destination would be a 2-night stay. Might not.

6 nights in Tokyo
2 nights in Takayama (possibly visit Shirakawago?)
2 nights in Osaka (day trip to Nara)
1 night in Koyasan
4 nights in Kyoto
1 night in Hakone

Seems like the trip to Haneda Airport from Hakone is not that bad at all so I've re-arranged a few things and I think I finally have it down! Thank you for your feedback! The next thing I need to figure out is if getting a JR Pass is worth it for us or not. Any advice based on this final itinerary?

That works. It's a good travel plan.

A 7-day pass won't work for you. A 14-day pass would depend on what day trips you would take from Tokyo or Kyoto, but it would have to be a lot.

Ok, a 7-day pass, just maybe. Like one the day after your first night in Kyoto you took a day trip to Hiroshima.

If you're in the tokyo area for 5 days i would make a day trip to either areas near mount fuji like Churreito. And then i would also make a day trip to Kamakura as it is absolutely beautiful!