In all games other than Mega Man 9 and 10 Bass seems to have different proportions than Mega Man. They could still make it work, but I think Proto Man is the better pick. Should they choose him I think the best way of tweaking the moveset would be to have Proto Man raise his shield after jumping while not attacking. The shield would reflect projectiles at a 45 (upward) degree angle. Proto Man would also take 1.5x damage. As for his actual attacks, his Neutral Attack, Forward Tilt, and Neutral Aerial should fire two, more powerful buster shots, his Up Tilt should be Knight Crush since he can't use the Mega Upper, his Dash Attack should be Proto Strike (a powerful K.O. move), his Down Aerial should fire a fist instead of Proto Man's actual fist since he has never used the Mega Arm, and his Up Special would be Proto Coil; a move that is the same as Rush Coil, but without the dog. Also, while Proto Man is charging his Forward Smash, he could hold up his shield to block incoming projectiles like he does in Mega Man 7.
This is my thinking as well. Though if it's at all possible Alph should totally have his Purple Pikmin reskinned as Rock Pikmin.
Simmilar to Alph, I think Ms. Pac-Man should also be an alternate costume. It'd sure beat the leg warmers and wing boots anyway.