I don't know about this. Characters like Zero and Dr. Wily are so different from Mega Man in both aesthetics and abilities that they wouldn't look or play anything like each other. Even Bass, a character that you had personal concerns with, is different from Mega Man both in the way he controls (having a weaker, rapid-fire buster, being much more mobile, and using weapons from the latter half of the series) and the way he looks.
The only character I could see this being an issue for is X, who is probably the most likely Mega Man character to join the battle, but that's only because Mega Man and X look somewhat similar. In terms of abilities, X would be a much more agile take on Mega Man's playstyle while keeping his projectile-heavy gimmick. Likewise, X would likely have some sort of armour mechanic to match his original game. Even then, their designs are distinct enough that you wouldn't really confuse the two. Capcom places Rock and X beside each other in marketing materials all the time, so they clearly have enough faith in their audiences to understand that these are two separate characters.