Who is the more powerful of the two?
Magneto's upper limit has varied wildly, going so far as to allowing him complete control over the EM field. He's ok in a fight, but largely depends on how old the body he's in at the time (since he's been cloned and regenerated so many times, hard to say at the moment).
Doom's got a much more wild powerbase. His armor is around Iron man tier (depending on whether you ask Tony or Doom), he's a sorceror capable enough to vie for the title of Sorcerer Supreme, he knows an alien mind control technique, and he's a fairly decent hand to hand combatant.
So while Doom's got more going for him, I'd say Mags has the theoretical higher upper limit. All the "god Doom" talk is whenever Doom is jackin' someone else powers, like the Silver Surfer, the Beyonder, the Molecule Man, etc.
That said, Doom would probably find some way to steal Magneto's power and then beat him unconscious with his own helmet.