Original characters. I've seen a few manga/anime and I'll be honest, so many of them seem to be tired cliches. With Fullmetal Alchemist, I don't feel like I'm reading the same thing over again, all the characters are unique and the narrative doesn't hop around miscellaneously. I loved the main cast and the villains were interesting as well. (Not to mention, every one of them was badass.) Each had a distinct story to tell.
Intense plot. Arakawa's research really shows in her work, so much detail is intricately woven together to create a compelling story that is able to stand on its own. Even the subplots are interesting. The revolving theme of alchemy helps in creating an interesting universe.
Great humor. While the story is dark and brooding, there are still some lighter moments and some decent humor that helps soften the mood. A typical volume ends with a few four-panel strips that poke fun at the story. Some running gags include Ed's stature and Alex Armstrong (who himself is a gag).
Drama. There's plenty of suspense that helps to develop the characters more. There are some pretty sad/touching moments, particularly in the last few books and even in the first ones.
The plot isn't stretched out too long. Unlike your fellow Bleach and Naruto, the author knows when to end the story. So many others become almost a chore to read, but FMA doesn't "kick the bucket" and has a pretty satisfying end.
Envy. This is more of a biased opinion, rather than an actual flaw in the story itself. He's the only character that just didn't need to be there. I was actually cheering when he died, I didn't get this feeling for the other Homunculi (the villains).