It's a complex mess of lots of factors. Economically, the CPI is extremely resistant to change over there. Companies apologize for raising prices by even a few pennies. Nationally controlled zoning practices keep residential buildings high in supply, and they're not treated as investments like a home in the US is, so a house will become worth nearly nothing in 30 years' time.

Obviously, there are pros and cons to this. Cheap housing, but no transfer of wealth to later generations through housing. Even if your parents die, the estate they leave you is subject to a death tax, so you lose even more of what wealth they might have built for you.

I think the biggest factor to do with the decrease in birth rates is that school and work are so demanding over there. People can't relax well enough unless they find themselves in the graceful employment of western-style companies. Not everyone is a salaryman, but enough that it makes family life challenging.

Aside from that, you've also got the brain drain of urbanization, where most rural villages are outright dying as people migrate to Tokyo/Osaka/Kyoto/Fukuoka.

All this said, I'd still live there in a heartbeat. You will never live in a more affordable, safe, convenient city as Tokyo. No other city even comes close.