It was a dropped ball. There are dozens of ways a recently-conquered country would inspire a local to rise up. Hell, the main character probably had access to some of those motivations but they weren't shown to be important.
I get the idea of a "blank slate" protagonist, even if it is a little...Bella...for my own taste. But the FF games are often about going after a massive authority -- a massive corporation, government, religion or god -- and the motivations of such a story should be clear. Nobody takes a molotov to a Wal-Mart without a reason.
Don't forget the lazy racism!