Well, if you aren't yet in Japan, but a Japan Rail Pass - it'll save you heaps and you can use most of the Shinkansens.
And on. Shinkansen you can go far in a week. My suggestions:
1) couple of days in Kyoto, if you haven't been before.
2) I really enjoyed Sakurajima just off Kagoshima on Kyushu. Great Onsen!
3) there are loads of temples on Shikoku. My recommendation: climb the 1500 odd steps to the top of Kompira sama
4) at the right time of year Miyajima just off the coast of Hiroshima is wonderful
5) loved Kanazawa & it's ninja temple!
Enjoy over 4 years ago
If you have 7days, I recommend
Tokyo(2 full days): Imperial palace, Tsukiji Fish market, Asakusa, Shibuya, Meiji shrine, Odaiba, Tokyo disney land, and many more.
Kyoto(2 full days) and Nara
Hakone(1 full day): if it is clear sky, you can see Mt.Fuji from Hakone well.
Nikko(1 full day): world heritage
Enjoy planning your trip! about 4 years ago