When I ask this question I don't mean between fullmetal alchemist and fullmetal brotherhood. I mean witch do you watch as a series.
Both series are in fact separate entities.
The series named simply Fullmetal Alchemist was created first and went in a very different direction from the source material once the basic premise was established. Brotherhood instead closely adapts the original manga in it's entirety.
Edward and Alphonse lost their respective parts trying to resurrect their mother, Scar and the Homunculi exist and both series start off in Lior but that's where the similarities end. Major details like the origins of the Homunculi and the overarching plot are entirely different.