General opinion is that the first anime has better beginning, like Brotherhood expected you to watch it first and wanted to focus from where the original branched from manga.
Myself, I dunno. Watched FMA years ago, and recently started Brotherhood because I was bored and had it bookmarked on YouTube. Haven't watched more than a few episodes, but it felt too shounen'ish for me. I mean of course it's a shounen, but some things felt out of place in anime while they are OK in manga (GITS while being a different beast has similar things and they didn't make it to neither anime adaptation - for better. I don't have any problem with them being in manga, though). And I remember liking the more serious atmosphere in FMA in general more.
But again, that was years ago.