I'm going to have to say Lust.
In the first anime, at the end she turned out to help the Elric brothers. And throughout the entire series she had deeper thoughts about humanity and what it really meant to be a human. She questioned her existence in the world and displayed a deeper, genuine side to a homunculi, and that they could possibly have human feelings as well.
However, in the manga, she was just down right evil. Straight to her death she was trying to do whatever it took to help Father.
But there were other characters who were pretty different as well.
In the first anime, Ed was very angsty, while in the manga he seemed happier and more willing to let loose.
In the first anime Riza was extremely monotone, and she didn't really have a personality. She was pretty boring. I mean, all I got out of it was that she followed Roy around and did as she was told. However, in the manga she displays much more emotion. When she thought that Lust had killed Roy she went psycho lol We even got to learn a little bit about her past with Roy and her father.
Roy is also pretty different. He seemed really angsty, as well. Sort of like Ed. He is in a state of depression over the Ishvalan War. However, in the manga, he carries on after the war, even though he may feel awful about what he's done. He also seems a little more carefree in the manga as well.
Roy x Riza - Edward x Winry - Ling x Lan Fan - Alphonse x Mei - Havoc x Rebecca