I don't know, maybe it's just my apathy for the X-Men, but looking at it from a pop culture standpoint, the Joker is far more important as a villain than Magneto.
i love the joker. obviously. he's iconic and awesome; constantly reinvented as hilarious, creepy, brilliant, etc. but he can't fully exist without batman. yes, he's appeared in superman or wonder woman stories, but its obviously some form of batman connection.
magneto is a stand-alone, awesome character. he's one with struggles you can relate to, whose viewpoints aren't really all that skewed from those who fight him.
he wins.
