I'm quite fond of Fullmetal Alchemist...both incarnations. I love that they kept the original dub cast for Brotherhood, but I didn't like the way they handled certain aspects of the anime: Envy, for one. I did not approve of how Envy ended up in Brotherhood, when he was such a prominent character in the original. Hoenheim really rubbed me the wrong way as well, and I think I preferred Scar in the original. I've never read the FMA manga, so I enjoyed a lot of Brotherhood (a lot of people I know who have read the manga told me not to watch it) but there were bits in the story that I really did not enjoy, which I think were prominent bits in the manga...mostly because it was either a character death or a pairing.
My favourite character...a toss-up between Alex Louis Armstrong (I just love his dub voice, it's so fantastically manly, yet effeminate at the same time. xD) or Wrath in Brotherhood, if only for that scene where he stormed Central Command by himself and took down a tank. That's just how awesome he is. Pride was considerably creepier in Brotherhood as well...