The perpetual economic stagnation.
Higher taxes coming down the pike (even now it is very high)
The aging population (more taxes on the working people).
1/3 of its workforce is not full time workers.
Sclerotic political system. (nothing is getting done).
Very closed culture.
You need to be bona fide Japanese-y to be successful financially in Japan (mostly).
Onerous regulations and rules.
Very crowded.
Very crowded train rides in the rush hours.
Too many toll roads. (What am I paying for my taxes?)
Build and demolish housing policy (Your home is like a perishable good).
Very backward looking legal system.
Strong sexism in place still.
If you stick out, they will try to hammer you down in line with the rest. (the collectivist culture
)
I know I have more. The above is a good starting point.