Osaka is my favorite place in the world!!
How long will you be in Japan for? Because, Tokyo, Osaka, and Kyoto are a pretty good start!
If you have the time, since you're seeing Osaka and Kyoto, you should check out Kobe, which is very near them both. Also, if time permits, try heading to Nara. In Nara there are tons of deer that come up to you so you can feed them! The peace pavillion in Hiroshima is really nice too. Also, Osaka has Universal Studios which is awesome!!!
Depending on the time of the year, You should check out Tokushima! I lived there for a year and at one point in the summer where they have an awesome festival called Awa Odori, and it's really really fun!
If your staying around Tokyo for awhile, try checking out Yokohama, you can do Tokyo Disney Land!
Hope that helps a bit! I'm moving back to Japan in the spring and I can't wait!!!