I just pray that the differences between Mega and Proto aren't that big, and that the weapons don't do different things for them ala X and Zero (it'd be even worse with Bass if he actually is a legit confirmed DLC).
Why would you actually desire that?
To me, the point of having 2+ characters, is to make for as many different playstyles. Rock could do more to play as he did MM5-6, while Blues could get something more original, thus making his appearance worthwhile beyond just having be a palette swap of Rock.
In other words, it only does more to give free replay value, as you'll have reason to go through the game at least twice over. Again, why say no to that?