My favorite less traveled areas are Shikoku, San'in Coast (Matsue/Izumo) and Kyushu. As a self-confessed rail geek, I have also done the rail trip from NRT up through Tohoku to Hokkaido and back, which was very enjoyable but a bit tiring. For that, I would suggest building in a couple of days at, say, Sendai/Matsushima, Hakodate, Sapporo or Asahikawa and maybe Aomori or Morioka on the way back.
I don't think even I would try Tokyo-Hokkaido-Kyushu-Tokyo by train all in one trip. That would be exhausting. With only a couple of weeks, it might be better to go either north or southwest, not both.