The fact that the japanese in general have no children at all makes this notable exception not be one at all. Humans are not meant to live on top of one another. To me the correlation between fertility and urbanization is a clear sign that living on the burbs is a plus for quality of life and the perpetuation of the human race. Cars are just a necessary tool for being a human in 2023.
There's more urban dwelling options than just skyscraper.
Low Japanese fertility appears to be a product of their work culture; you don't have time to go on dates if you leave the office at 10pm.
what modern skyscapers are doing wrong is putting in only large-footprint high-end retail (like department stores) on the street level, or nothing at all. A zoning change to require small retail stalls at the street level would go a long way to making cities more livable. And all those people living upstairs generate a lot of foot traffic to help all sorts of businesses thrive. (what I'm talking about overall is what makes midtown NY so unpleasant compared to other NYC neighborhoods)
...is not mandating proper insulation/noise-proofing.
Near the subway, and surrounded by historical buildings and nice architecture ... where an apartment usually costs an exorbitant price.
It's not that it's very expensive to build (well, it's not cheap either), it's that there's so little supply and so much demand.