This is the first survey for a while from goo Ranking not featuring a long list of quite unknown to me celebrities, a look at which prefectures in Japan Japanese themselves might want to try living in.
I’ve lived in a grand total of three (out of 47) prefectures, which I see all feature in the top ten here. In my opinion, Hyogo is underrated; Kobe and the surrounding area are very livable, with a lot of history of foreign settlement from when it was a major trading port. Osaka is also great, but I understand that Tokyo people are quite put off by the image of the locals. Tokyo is my current abode, in a suburban city, but I wouldn’t want to stay near the centre, but like capitals anywhere, the roads paved with good always attracts.
For where I’d like to live, Fukuoka seems attractive, as does Nagasaki.
For the top ten here, everything rusts and/or gets covered in mould, Hokkaido is too harsh in winter, and Kanagawa, or the main city Yokohama at least, is pleasant, but from my standpoint, a cheap copy of Kobe. Kyoto city has too many tourists (well, not currently, of course) to detract from the rich cultural heritage.
Note that I am mostly focusing on the major built-up areas in the prefectures, as once you get into the countryside the differences between many prefectures disappears. Even Tokyo has about a third of its area taken up with deep, deep countryside, and over 1,000 km offshore there are sub-tropical islands:

Where would you like or dislike to live in Japan?
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