Magneto is the typical "sympathetic individual gains great powers" trope turned on it's ear. He has a moral ambiguity and incredible personal complexity (his motivations driven by survivor's guilt and the fact that he paradoxically insists he is a "realist", when in fact he is an extremely idealistic and romantic character, among many other aspects of his personality) feeds into a very realistic characterization that makes the character stand out in the typical super hero genre. Characters like Magneto are more normally found in dystopian SciFi novels and more artistic graphic novel endeavors like the Watchmen.

(I also agree with DirtyToyTrunk above that his close friendship with Xavier, which has withstood beatings that otherwise would have two people murderously hating one another, is interesting and fun to read. No one but me would read it, but I would love to see a miniseries of just the two of them talking. That would be such a facinating conversation.)

Under the right writer's pen, Magneto is a complex anti-villain who calls the perceptions of heroism and real world events into question.

Under the wrong writer's pen, Magneto is a stock madman who does not stand out from the herd of evil bad guys in the slightest and actually pales in comparison to villains like Sinister and Cassandra Nova.

This is the problem with being a fan of the character. In the last ten years Magneto has been handled by writers who loved him and writers who openly admitted to hating the character, making his characterization swing wildly. It's like being a Wolverine fan and not knowing if Logan is going to be kicking butt or picking daisies from one appearance to the next.

Given Magneto's importance in the M.U., the fact that he has been placed as the 9th greatest comic book character on lists compiled by both Wizard and Empire magazines, it's more than a little surprising that editorial has allowed the character to be handled so clumsily in recent years. Allowing writers to wrestle so openly over the characterization does not help the audience invest in the character and take him seriously. The fact is the character has been developed far too much to allow writers with a Silver Age fetish to reset the clock back to 1971, and Marvel should not be allowing that.  Magneto did not shoot to stardom until Claremont made him a three-dimensional morally ambiguous anti-hero/anti-villain. Marvel should not be throwing that away on personal child childhood fanboy thrills.