I agree that Kyoto is a beautiful place to see - there's culture falling over itself round every corner - fantastic. I think you can stay in Osaka and travel to Kyoto during the day - that's what I did when I went down there and it was only 30 minutes or so to Kyoto as I remember - not long anyway.
Tokyo has some must see sights for me. If you love funky places try Odaiba - so much to do there is something for everyone - future science museum, hot spring baths edo style, shops and shops and shops, joypolis a big game and ride area right next to the shops and a big showroom dedicated to Toyota where you can even drive one of their cars.
Nights out - you should try Shibuya or Shinjuku if you don't want to be where all the foreigners are - generally they end up in Roppongi. Good venues can be found here
Secobar Shibuya Tokyo (Nightclub) check the links down the left : )