I've always read it as at least a little bit a comment on the Iraq war, but what's it's deal? It's the only anime I can think of that climaxes with a military coup, and its cool that mustang wants to put people on trial for war crimes, but then he gets in power and doesn't do it.
It's also just got a whole plotline about racism, but it feels slightly off? Like minorities are okay if they save your life.
Wait, aren't there two different versions? Because I remember the political stuff being more subdued - the version I remember was fun magical adventures mixed with sad magical adventures.
EDIT: More "subdued" I guess in the sense that it didn't take root in my brain - the government was magical evil fascists but I don't recall the show really digging too deep into it.