Tokyo schools for foreigners

Tl;Dr; looking for primary schools and beyond for foreigner kids around Tokyo. Need everyone’s wisdom.

My wife and I are foreigners (Indonesian and French), we have two boys in kindergarten, and we are very worried about their education from now on.

The three options we see are as follow:
1) Japanese system: we are worried that
a) our kids will have to go to juku (taking most of their free time, and costing lots of money),
b) they will have to join clubs that are a bit extreme (training from 6-7am many mornings, crazy professional equipment required)
c) they may be bullied for being different (not japanese, half south east Asian)
d) they may be disadvantaged for not being native in Japanese (we parents are fluent in Japanese but we do not speak Japanese at home, and we would not be able to tell whether an essay in Japanese is good or bad)
e) the teaching level and content seems a little low for some things (like foreign languages)
2) French school in Tokyo: expensive (1.5M yen per year?) and maybe inconvenient in terms of holiday and school time.
3) International schools: just outright out of our budget (saw 3-5M a year)

So we are wondering if you guys can either point out any misunderstanding we have, tell us about your own experience, or tell us about awesome schools which can be good for our children.

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