LogFAQs > #912195945

The first one is pretty good with its dark theme and high concept ideas, as well as a great expansion on the homunculus idea and tying it to the show's lore.

The other follows the manga from start to finish and has an entirely shouneny feel, with lots of fight scenes, and some creatively done battle scenes sometimes for certain characters, especially with the homunculus powers combined with the good guys' alchemy.

So it depends on what you're looking for. I'd say to watch both, which gives you about 100 episodes of pure FMA goodness. It's just such a great anime, the best.