I think the way to plan your trip, is to find out what you want to see. And then see if you will be traveling allot or not. Japan has allot to offer.
On my holiday in Japan I spend a week in Tokyo and a week in Kyoto, and after that 2 or 3 days in allot of different cities and towns to see the major tourist attractions. This way you see allot of the country and it's culture, but you miss the peoples aspect. So spending some time on the Japanese people alone would be great (in my opinion). Nightlife in Tokyo !!
