I've been in Kyushu, in the south.
Japanese railways are indeed amazing, but it should be pointed out that peripheral routes are being dismissed everywhere in the country side, often isolating people and killing places.
Infrastructure is also dated in many places.
It's not a criticism to Japan, I think they are just facing the fact that many people move to the cities and the country is on a population decline as well.
They are facing this very masterfully.