Wow, those are some great places to get to if you have a lot of time. By a lot of time, I mean like a good month! Three weeks at the least, along with a rail pass. I'd recommend if you have less than three weeks, stick to the Kanto (Tokyo, Yokohama, Nikko, Kamakura, Hakone) and Kansai (Kyoto, Nara, Osaka, Ise) areas. If you can, get to Hiroshima/Miyajima for a few days. This is unless, of course, you have a specific agenda (ie. skiing, hot springs in Oita for some reason, your cruise ship from Dubai is docking in Nagasaki/Fukuoka, etc.).
Going to Kyushu, Tokoku, Hokkaido, Shikoku, etc. would be like going to Colorado in America, or Scotland in the UK. Definitely worth a visit, but not essential on a general tour.