I think you are underselling Superboy-Prime as well, but meh, I'll go ahead and clarify. Both have absolute zero attacks, both can hurt each other on the molecular level, Mega Man can turn invisible, SPB has Supersenses to compensate, and both have insane durability. Mega Man takes the edge in versatility, but not by enough for me to give him the win on that alone. So what does did it come down to for me? Partially the battle description. Both being in character, but having knowledge of each other, makes me believe SPB would go for kill shots first. If that doesn't work, and it is unlikely it would, it causes an escalation that I see ending up in a brawl. The kryptonian martial arts allows him to predict movement, i.e., more easily avoid attacks because he "knows" what is coming.
Has nothing to do with him being evil, just the way I see it playing out. II don't even see anyone making that argument, unless you meant my Ruthlessnes one, which is a mischaracterization of what my argument is. It is part of a whole of why I leaned toward Prime and not MM.
Though I am reconsidering my vote now, mostly over soul manipulation. I can't recall Prime ever showing any reisistance to that, and that is a has that is a big problem, cause there isn't a counter or balance to it for him.
