If I could change something, I'd change the way the anime or the movie ended. I want a utterly happy ending, with both Elric brothers with their memory on the Amestris side of the the Gate. Also, I would have really liked some reason for why Roy suddenly felt the need to go off to the North, because while I can fanwank it, I little more reasoning from the writers of the movie would have been nice.
SPOILERS FOR THE END OF FMA AND THE MOVIE!