Why would the level design have to suffer?
You design the levels for Mega Man to go through.
Then as a BONUS mode you can select bosses as playable characters.
They would have their own attributes:
Different jumping/control in water,
Different Attacks obviously,
Different Slides and such,
Possibly Double Jumps.
The bonus mode would be about trying to select the best character to get through the stages...not just the best weapon to beat the bosses.
I understand, that it wouldn't work perfectly...that is why it is a bonus mode. And if you are worried about selecting the wrong character for the level...another means they COULD do it, is by doing it in a Challenge mode.
There would be several individual challenges within levels after you beat a game.
Like, get through a part of a stage without taking damage.
Other challenges could be to beat specific levels with a boss character...and then the designers are putting that boss character in the level KNOWING, that character can make it to the end of the level.
Problem solved...and replay value enhanced.