I like them the same, and they both are really good.
FMA (2003) is basically it's own story with the same basic characters. almost like a Fan Fic. It's a lot longer (almost 3 times as long as brotherhood) and last "Episode" is a full length movie.
FMA Brotherhood (2010) sticks with the Manga, but is short but just as good as the 2003 series.. IMO