It's a matter of opinion, as many have already stated.
I enjoy them both, but I prefer Brotherhood. Animation standards aside (because Brotherhood had a bigger budget, I do believe), the story doesn't seem...well, rushed. I like the original, but it had this feeling like they just made a bunch of stuff up so they could finish quickly. This didn't really hit me until I had finished the manga though.
Also, I loved the military characters, but after about halfway through the original, most of them just got tossed by the wayside, it felt like. They were there, and they did stuff, but they didn't get that much development. In Brotherhood, they get development, and several are directly involved in the endgame.
I prefer Brotherhood because the ending's better and ALL characters are important and get at least some back story (including minor ones).