I went there last summer with a friend, for a bit more than a month. It was way better than expected. And I had high expectations.
First Week : Up to the North (Touhoku)
Arriving at Narita, we went directly to Nikko (magnificient place, Tokugawa's grave), then Sendai, Yamagata (and Yamadera, a mount/temple not far from the city), Shinjou, Sakata, Akita (for its Kanto Matsuri), Morioka (Sansa Odori Matsuri), Hachinohe and finaly Aomori (Nebuta Matsuri).
Second Week : Traveling to the south (Chubu-Kansai-Chugoku)
After Aomori's festival, we figured out that we didn't have time for Hokkaido so we didn't go further.
First destination while coming back down was Utsunomiya (where we were invited to eat suchi at a random jiisan's home, whom we had met in a train while going to Sendai), Kanazawa, Kyoto, Nara (for it's deers), Osaka, Himeji (for it's castle) and finally Hiroshima, our very favorite till then (for its food :p) (while there we went to Miyajima, a marvelous island in front of Hiroshima).
Third Week : In the South (Kyushu- Shikoku)
First stop after Hiroshima was Fukuoka/Hakata (where we went to a memorable baseball match between fukuoka hawks and osaka/kobe's orix buffaloes that we won), Karasu (at a friend's), Kagoshima (for Sakurajima), Kumamoto, Beppu (for all the onsens), Tokushima (for the Awa Odori Matsuri <3) and finally we went way back to Kanto region, to Gotenba.
A little break : 4 days of adventure
Gotenba was actually our destination near Fuji as we planned to climb it. and so we dit during the night, a stormy one, taking the subashiri rout. At that point, the railpass was already out of date, so we decided to go to Tokyo by foot, took almost 2 days : Gotemba-Odawara (38km, 1rst day), Odawara-Yokohama (61km, second day), couldn't go further, but well, it was pointless once at Yokohama, the landscape was already urban.
Last week : Tokyo !
Well a lot of things there : Nakano, Shinjuku, Shibuya, Harajuku, Asakusa, Akihabara, Ueno, Ikebukuro, Ginza... But well, Tokyo was like a whole new country, didn't have enough time.
Now I need to go to Hokkaido, Okinawa, and the japanese alps before being able to say "I've travelled all around Japan". And then I need to live there for like 1 year or two, in order to deepen a bit more the experience. And think i'll be satisfied then and I'll be able to move on. That's the plan.