All of your complaints sound like someone who is projecting American values and behavior onto another culture.
> Or new local businesses cannot start because they can't buy property limiting options for consumers?
Are a lot of new local businesses starting up in America's suburbs? Is it a problem to have the same shops operating in the community for decades if they serve the community's needs?
Even in Manhattan I saw 'shops' which seemed to have a similar square footage to my bathtub; if there's an opportunity people will find a way.
> And public transit stops become noise and litter parties.
If you have garbage cans at your transit stops and your populace are respectful towards each other then this is also not a problem. If your idea of a transit stop is somehow also some kind of rowdy social event then the problem is not urban planning.
Fundamentally though this is a common American attitude. Look at something that's new and different and say "This would be bad for these reasons", ignoring the fact that dozens of other Western and Eastern countries with dozens of different cultures and behaviors all do these things and it all works out fine.
It's the same as the argument about health care. Socialized medicine would be bad for reasons X, Y, Z, even though if you look at countries which have socialized medicine and a similar standard of living you'll see that not only do those countries not have those problems but also those countries have better health outcomes, longer life expectancy, and more efficient healthcare.
You say that none of this stuff would work in "a culture that isn't Japanese", but what you really mean is that it wouldn't work "in a culture which is American", so maybe that's a good place to start looking for things to change.