Given his recent whacked out appearance in Uncanny #500, I really am hoping Magneto turns out to be a skrull.

It makes sense. From the beginning planning stages of the Invasion, the Skrulls were concerned about the large Mutant population uniting against them. Putting a skrull next to the High Evolutionary to sabotage any attempts to repower the mutant species would be in their best interest. And as leader in the mutant community, Magneto is ideally placed to keep the mutant community from uniting. That explains his rabid factionalism in #500, which would be part of the plan to keep the mutants divided and leaderless.

It also explains Magneto's lack of interest in repowering the mutant species until now, his rather random behavior since the helicopter exploded in New Avengers #20 and he disappeared, and how the heck he got to the mainland from Genosha without his powers...

What is awesome is they can kind of hold this door open for a while. Magneto is hated by the heroes of the M.U. I can totally see a massive break out of a Skrull holding facility...and the heroes leaving the real Magneto behind as a "lesser evil". That way they can put the character on the back burner until writers and editors figure out what to do with him post M-Day. Meanwhile the writers with a Silver Age fetish (that can't be bothered to go write for the Ultimate universe) can write Magneto as bad (and I mean that on multiple levels) as they want to.