Magneto (18) +2
Charles Xavier (172) -2
I just want to say I love what the prequels have done with Magneto and Xavier. Both of them have been made far more exciting (not necessarily to say better) characters and both deserve to win this.
Though my overall knowledge of the characters from comic history has me lean toward Magneto as the greatest X-Men character that was listed here from the beginning. I do understand the predisposition these boards tend to have for the "good guys." But in my opinion, Magneto has always been the good guy.
I think, were you to have told the original comics and called them "The Brotherhood" and shown them battling their way through humans that hate and fear them and the "Evil X-Men" that stand as an army for the violently intolerant humans, most people would understand why Magneto is the hero of these stories.
Xavier is wrong. There is no endgame where humans are still alive.