Sephiroth, but he would require his own moveset
Akuma, easy Echo Fighter for Ryu (alongside Ken)
Eggplant Wizard, but would require his own moveset
Giovanni, but would require his own moveset (could switch between Persian, Nidoqueen, and Nidoking like Pokemon Trainer)
Bass, could be an Echo Fighter for Mega Man
His Final Smash would have to be his own though. Maybe turning into Super Bass (from Mega Man7 and 8) and firing all his Robot Master weapons at once. After all, Bass does love overkill.
Hero vs Villian
Cloud/Geno vs ***Sephiroth
All Fire Emblem vs ???
Mewtwo's not a villain, he's more of a difficult challenger to other Pokemon.