Starphoenix
How Long Have I Been Asleep?
I've always seen Mewtwo more in line with this guy.Mewtwo is essentially the Akuma of the Pokemon world.
Waits until it sees a worthy opponent, and fights to the death to test their strength (or in Mewtwo's case, to the faint) if they accept the challenge.
Both are ruthless, but not outside of reason. They have enough power to essentially cause mass genocide, but are not bloodthirsty murderers, and only show their power to those they find worthy and are willing to take them on, knowing full well they may not survive.
Whereas people might consider them villains as a result of their way of life, they are not villains.
That being said, Melee established Trophy Mewtwo as a villain in the Smash world, so future Smashes will probably do the same.
As for other villains, I'm trying to think of who all else could fit.
Bowser Jr.
King K. Rool
Ghirahim
Medusa
Hades
Ridley
Dark Samus
Porky
Masked Man
Black Shadow
If we wanted to talk about bosses I could probably think of some more.