You are correct that I tend to wind up in little business hotels in places like Matsue or Kochi. I was thrown off by the poster's reference to "nice" hotels like SPG or IC and the desire for similar places in smaller cities. If one wants an IC, I stand by my advice. I see, however, that the poster has clarified and such accommodations are not really necessary. In that case, I am with you. On my last long stay, I actually stayed a few nights in Nara instead of Kyoto or Osaka as well as several other other somewhat out-of-the-way places. Not a single night in Tokyo, Kyoto or Osaka.

If the poster is ok with smaller, local hotels, then I think the "hub-and-shink" method (love that by the way) is not the most efficient or enjoyable way to see Japan.