In my head, Brotherhood IS the original... the original story. Although I saw the 2003 anime before I ever read any of the manga or heard any rumour of the Brotherhood version, while I loved so much of it, I felt it was wrong somehow. Brotherhood, being based on the manga, got it right.
My biggest problem was when Ed discovers (huge spoil alert here for any innocents who haven't seen all of the 2003 version) that alchemy is based on energy from people who die in the version of Earth connected to their world. This means that ALL alchemy derives from the death of others. So ALL alchemy is inherently evil. Yet even knowing that, Ed returns to Amestris from the other side of the Gate, and uses alchemy to fight Dante and the others, then after being going through the Gate again, and once again returning to Amestris, he STILL uses alchemy. A lot.
Alchemy in the manga and Brotherhood is either derived from the Dragon's Pulse-- energy that goes through the planet-- or from tectonic plate shifting.
So in my view, yeah, Brotherhood is way, way better than the 2003 version. Although Hughes's death makes me cry in both. crying