i voted for kefka and sephiroth - they seem the most evil to me.
ganondorf and bowser... i think we already saw that in super smash bros. melee in challenge mode, along with mewtwo, and bowser was in his "giga" form at the time. a pretty cheap team, but not for global domination.
and since i grew up on sonic and my best friend grew up on megaman, he thinks a combination of the two would be rather pathetic, considering how most of the bosses in the original sonic games were easily beatable, and how he owns the hell out of the megaman games (which i still have trouble with). but, as long as they didn't develop a robot/vehicle that couldn't easily be hit 8 times and die, or had only 2 alternating forms of attack (lol), i think they could be a close second.