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.
There's something to be said about Entryism, as a great deal of the story revolves around Edward's decision to join the military and the consequences of that decision.
There is also something to be said regarding the cost associated with power. The Equivalent Exchange Theory that underpins Alchemy and the efforts power-seeking individuals make to circumvent this rule form the backdrop of nearly every character in the show. The big reveal in the show boils down to
Full Metal Spoilers!!!
the potential for unlimited power being prefaced by the necessity for limitless cruelty, a la human sacrifice on a national scale being necessary to create a "flawless" Philosopher's Stone.