I like both a lot, but for me personally, Brotherhood (manga) edges itself out a bit better due to my own preferances. Considering what BONES had to work with for the first series, they did an immaculate job, and its easy for us jaded fans of Brotherhood and the manga to scrutinize and overlook its certain aspects that are frankly quite brilliant. As for what sells to me better regarding Brotherhood, I've always been a big fan of fleshed-out, fully-realized worlds, and I get a grander sense of what's going on; there's more at stake here, though that doesn't inherently make it better than the original anime's more tight-knight, personal story of obsession and despair. As far as villians go, I don't really regard Father or Dante as being that great; it's the secondary ones, the homunculi, which stole the show for me in both instances, most of them having fully-realized characterizations and aspirations which made them unique and emotionally resonant; the original series made a bigger point of making them objects of empathy, while Brotherhood's rendition de-humanized them in certain regards, though it still shines through for me better in this case, as while Envy, Lust, and Sloth lost a bit of depth, Wrath, Greed, and Pride got a huge boost to their own characterizations (Wrath ended up being my favorite overall character in Brotherhood).
I could go on, but to me, they're both great. I haven't revisited the original series years, but I feel It's about time I gave it another viewing -- short of the moive, that is.