[Crazy Jetty]

I think in straight match-ups where you pit characters with simular abilities over one another, the marvel characters win hands down every time. It's a joke to think Vader could beat Magneto, for all the reasons already put forth.
Though it gets genuinely interesting when you pit characetrs who aren't the equivalent/equals. Spider-man vs Darth Maul. Captain America, or Thor vs Darth Vader. When the hero is at a seeming disadvantage, like Cap, or so different, like Thor... then you get into genuinely interesting possibilities.

I call it though for Marvel. Here's why.
DOOOOOOOOOOOOM! I think Doom's magic would compensate for the Force. Which is enough to fend off Vader's force attacks. His armor puts him at least on equal footing with Vader, if not easily besting him. Leaving Vader with only his lightsaber as his primary weapon. But, I don't think it'll go down that way.
Vader is forever a toady. That's all he's ever been. I think Doom would lure him away from Palpatine, and the two of them together would take over the Empire, with Lord Doom master of all.