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.
It's main message is to always keep moving no matter how bad things get, and to not lose your humanity in the pursuit of power or control. The messages about the Ishvalans are more that genocide is never for the advantage of the citizens of the country committing genocide, but for the goals and power of the rulers. I think you're forgetting that germany committed a few genocides in Africa and the Middle East before WW1, which makes the loose metaphor more clear than trying to impose american actions from much later onto it. There's also a lot of "don't be blindly obedient to authority, and fight your government if it is evil" messaging, which is vague and not as radical as we would like, but better than most liberal shows.
The main reason I always connect it to Iraq is the timing, the series started in 2003 so it's just right there.
I get that, but it just doesn't add up quite right. Iraq wasn't a US colony before invasion, but germany did hold colonies wherein they committed genocides to maintain their power and access resources.