Adult Swim interviewed the director of the FMA anime and here are a few excerpts:
"SM: In the second half, the series takes a departure from the original manga, and the story becomes an original creation from the animation staff."
AS: How did you develop the storyline for the second half? Did you know that you would have to create a story different from the manga from the beginning?
SM: Yes, you see, the original manga had only been sold for a year, so there were only three volumes available, so we knew that there wasn't enough to work with, so from the start, we were planning on probably going with an original storyline. Several times, we presented Miss Arakawa with the plans for the storyline that we had come up with for the second half of the series, she looked at them and discussed them with us, had meetings with us, that's how we created it.
(from a convention panel): What's the most difficult part about working on an anime?
SM: Well, I've been able to work on two animated series based on long-running manga series, Shaman King and Fullmetal Alchemist, and the most difficult thing with on-going series like them is to create, in just one year, with about fifty-one, maybe fifty-two episodes, an encapsulated storyline. Within that limited span of time, you have to take all of the interesting points from the original manga and put them into the series. You also have to work with the creator to come up with an ending original to the anime. That, and quality control.
I think Full Metal Alchemist is really a great show and I'm hoping Adult Swim gets to air the movie ^__^