Kyoto is fun. I spent a month there...I stayed in a guest house near gojobashi (5th bridge)...
ummm i like visiting temples/shrines and other historical sites...
if you like hiking, and don't mind spiders...(they scare the crap out of me but I hiked the whole thing anyway) I'd recommend visiting Fushimi-Inari shrine in Kyoto..its is one hell of a hike..took me all afternoon to walk the tori path, but i thought it was cool.
Also...visit Kyou Mizu dera, Gion. The imperial palace is okay but, Nijo castle is better. It is a very cool city to wander around...
for fun shopping try Teramichi shoutengai...it is near Sanjobashi (3rd bridge), lots of cool shops there. spent lots of money..lol.
and you can easily jump the train to Uji to visit the pheonix hall (Byoudin Temple), or the train to Nara to go to Toudaiji from there...Toudaiji is cool cause Nara park is full of deer and you can feed them crackers you can buy from the vendors.
Tokyo: i was only there two days...I'd suggest the tokyo tower (has a cafe on the first observation deck, a tasty place for icecream,)
Ueno park for cherry blossoms...you're going in march right, might be too early?, Akusakusa , Akihabara, and shinjuku. Roppongi if you want to go to any concerts/clubbing...
oh and Kyoto might still have snow and be cold!!...while tokyo might be warm...
unfortunately all i saw of osaka was the airport..lol