I agree that while you may have input, it's really your wife's call. Having said that, there are so many nice places to live in Japan. If I were to move back, I'd probably go somewhere in Kansai, I think. Mino-shi is pretty nice, and not too urban. I'd stay in walking distance of Kitasenri-eki. Kobe is nice, too, but my only experience with Kobe is as a visitor.
If I wanted to live somewhere cheaper, I'd just go out to the countryside. There are towns that will give you property if you move there, and other such deals are out there, as well. I remember that land was pretty cheap in Shizuoka prefecture about 10 years ago or so.
I could actually make a case for a lot of places in Japan. There's so much character everywhere you go. But Kansai has jobs, it's fairly centrally located, and it's where I got my start in Japan, so my vote is for Kansai. HANSHIN TIGERS FOREVER!!!!!