So lets pretend Charles and Erik remained BFFs and never had that big falling out. Assuming they are able to bring in their respective followers (Xavier with the X-family, Magneto with the Acolytes) Can Marvel earth stop them?
To avoid possible argument, we'll see Magneto was the one to convince Xavier over to his side of thinking.
Quicksilver's wish made House of M happen. Otherwise, Magneto would still remain a wannabe world conqueror. That's why Magneto was pissed at Quicksilver when he found out about it. Not because Pietro exploited his sister's power, but that Pietro thought of it first. It's this kind of thing that makes Magneto second rate compared to Doom. By the time Magneto comes up with an idea, Doom would've already done it.
Actually, Magneto's the one who refered to himself and Doom as Homo Superiors. You know Magneto's afraid of Doom when he elevates a non-mutant to Homo Superior status. Doom would've pimp slapped the mutie for anything less.
Honestly I think it'd be closer than people think. They would likely set astroid M as their base, which is a little outside of a dampening field's range. From there Magneto could use Stark's own satellites against him. Not to mention they would be getting more mutans to their cause if they were united. Also Im thinking Xavier with cerebero could cause mass damage on earth. As for the Doom vs Magneto comments, that can kind of go either way. Yes Doom has simply turned off Magneto's powers before, but they'd have a lot of pretty impressive minds working with them as well, and could possibly counter it at least once (before Doom made a better version), not to mention classic Magneto used to make a joke out of the Avengers (see scan of him magnetizing Thor's hammer and sending him away.)