Well, Meta Knight turns out to not be the main bad guy, and Bowser isn't evil enough to be doing all of these things on his own. So as far as evil Nintendo villains go, we're down to Ganon, Mewtwo, and Ridley, so someone's got to be over looking them all, and I highly doubt it's that Ancient Ministy guy. He seems too terrible of a villain. I'm thinking he just runs the army, while Ganon, Mewtwo, or Ridley runs him and the other Nintendo villains.
EDIT: Hey, playing Ocarina of Time and everything, who would of ever thought that one day, we would be seeing a Zelda character watching a Plasma Screen TV? XD