Hey,
You guys are going to have a blast. September is also a nice time, though it still might be slightly hot in the beginning of the month.
If your interest is the major cities, you will need more time in Tokyo. Out of the 2 weeks I'd say at least 5 days. Then you can take the bullet train to Hiroshima for one night, and work your way back to Tokyo through Kyoto, Osaka, Kobe, etc.
If you give us a better idea of what you are looking for, people here would be able to give you specific sites to visit.
Meanwhile, I suggest you take a look at my blog (
Smart & Cheap Japan Travel) where you can get ideas on things to do and see and stuff to eat (food should be one of your main focuses on your trip to Japan!)
Josh