Japan is an amazing country, so many contrasts between the super modern and traditional. And very law abiding and safe. We lived there for 4 years in the 90's and make a trip back usually once a year. My husband teaches Japanese and every two years we take a school excursion of 26 students (13 - 17) for 2 weeks. Next one is April 18 - we self organise and run the trip ourselves so I'm in the planning stages now :) I love seeing the country through the students' eyes, it really makes me appreciate everything afresh!
Tokyo is a great city for walking, lots of little side streets to explore. You will find the best restaurants off the main streets.
You can do a day trip to the Fuji national park (google Hakone Free Pass), lots of interesting transport on the circuit - zigzag railway, cable car, ropeway and pirate ship! There are some spectacular views of Mt Fuji if the weather is kind.
Kyoto is beautiful with so many lovely temples to visit. A couple of other must sees in Kyoto are Arashiyama bamboo forest and a day trip to Himeji castle about 45 mins by bullet train. This year we are travelling with friends and are doing something new in Kyoto. We are hiking from one mountain village to another (about 2.5 hours) and will be having an onsen when we reach our destination. It will be good for the sore legs!
Also, consider getting a Japan Rail Pass. We picked ours up last weekend and it was $327pp for 7 days. We are only going to Tokyo and Kyoto and it was a saving of around $300. You can check train times and prices on hyperdia.com which is the Japan Rail network site.
It doesn't matter if you don't speak Japanese. Most signs are also in English and everyone is so helpful and gracious.
Sorry, I've prattled on a bit! Jane x