We just got back on Sunday fro 5 weeks in Japan of which we spent just under 2 weeks in Hokkaido, 2.5 weeks in Tohoku and a few days in Tokyo at start and end.
We self-drove pretty much all of it except the Tokyo days. (We had to book two rental cars since I couldn't find any that would let me keep the same car for both Hokkaido and Honshu).
In Hokkaido we really enjoyed the national parks (Shiretoko and Akan-Mashu). Our overnights were Kushiro (1, we flew up and picked the rental car up the next morning), Utoro in Shiretoko (2), Akan (2), Asahikawa (2), Sapporo (3, from where we visited Otaru and Yoichi as well), Noboribetsu (1), and Hakodate (2).
We returned the first rental in Hakodate, took the shinkansen to Aomori and got another car the next morning. Itinerary was Aomori (1, but also visited Mount Osore from there), Lake Oirase Keiryu (2), Nyuto Onsen (1), Kakunodate (3, did some day trips), Ginzan Onsen (1), Sendai (2, also visited Matsushima from there), Aizuwakamatsu (1), Obuse (3, did some day trips), Matsumoto (3, did some day trips).
Many of the transfers from place to place and also the day trips allowed us to visit a whole load of additional places, including those I'd noted for kokeshi doll museums and making, ukiyo-e museums, particular food experiences and so on.
I can help with questions on the itinerary, the places above, the car rental, hotels, sightseeing and anything else you would like.
Let me know if you have specific questions I can answer.
by YouSayWotNow