I have been living in the inaka for 8 years now and I always laugh at this kind of articles. They only focus on the core areas of Tokyo, Osaka, and a few big others cities, and forget to mention that outside of those areas the whole country is just endless urban sprawl of the ugliest, soulless cities you can imagine.
This article is specifically about its most livable cities. Why would you expect them to discuss the cities people don't want to live in? Every country has plenty of these. The point is to show the things that make a place livable, not to show all the ways a place isn't.