I vastly prefer Brotherhood to the original version, personally.
I'm a fan of the series (was Kimblee for NDK09, want to make a Brotherhood version for '10 or '11), and I watched the entirety of the original anime. Then someone showed me an online chapter from the manga, and I was instantly hooked. I read every chapter that had been released in America online, and I can't say the original impresses me anymore.
To be honest, the "original anime" barely has anything to do with the Fullmetal Alchemist series. The characters and the plot are watered down and deviate so far from the original, it loses a lot of the intensity that the real series was supposed to convey. Brotherhood, on the other hand, has thus far followed the manga down to the dialogue. The characters are more unique and developed. To be honest, the first anime series is just a disappointment to me now.
Plus, it's longer. Who can argue with more FMA episodes? x3