I'm sorry, but anyone who thinks that Mega Man takes this one has NO IDEA what he's talking about. Sonic is a far more versatile character (even if you take into account Mega Man's powerups, most of which are simply alternate shots that are slow and easily dodge-able and are only useful in-game because the enemies' AI isn't programmed to dodge them), has far more impressive feats (he often beats mechs that are bigger and deadlier than MM, and even took out Perfect Chaos, who MM can't even touch, without using any emeralds), and is one of the fastest video game characters, in contrast with Mega Man, one of the slowest ones. Sonic should be able to easily dodge all of MM's attacks. The best bet MM has is using Flash Man's ability to stop time, but even then, he can't attack while time is stopped, so I still don't see how he's going to harm Sonic. In contrast, Sonic can stop time using a single emerald and still perform any of his attacks and moves meanwhile.
Bottom line is, it doesn't matter whether there are any emeralds or powerups involved, either way Sonic takes this one.
If you disagree with this post, answer the following questions:
1) How is MM, with his slow walking and jumping speed and slow shots, going to harm a hedgehog who can move faster than sound? No, Quick Man is nowhere near as fast as Sonic.
2) How is MM going to defeat Perfect Chaos by himself (ie: without powerups or items), like Sonic did? Heck, even with his powerups and items, I don't see him taking PC out.