Yeah, Kyoto is more like a weeklong excursion. It is utterly awesome but I would feel bad if you had to rush through it and missed, say, Kiyomizu-dera, or Fushimi Inari. Hakone, on the other hand, is a tourist town... I've never been there but I'm guessing you could spend one night and get back to your hotel.
As for Tokyo itself, yes, I'm toying with the Ghibli Museum - worth it, in your opinion?
It's very small, so you shouldn't expect Disneyworld, but it's an extremely well-put-together museum if you're willing to suspend feelings of childishness and enjoy Ghibli. I enjoyed the movie. Also, it only takes three hours at most to look through, and if you're smart you can take a walk through the surrounding park as well. It's a nice break from Tokyo.
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