Hmm, this talk of villains gets me to thinking. "Classic" villains are established early, present many threats to the hero, and are thwarted by the hero and his allies in the end.
So how about Haruhi as the villain? It may sound strange, but work with me here. C'mon...
Spoiler for ...imagine the possibilities:
"I am your father."
"No. No. That's not true. That's impossible."
"Search your feelings. You know it to be true..."
"Nooooooooooooooo...."
The villain gains power, and holds our hero and the Scooby Gang in her thrall. Then in Melancholy 4 there's this weird plot line where Ryoko Hinckley Jr. tries to assassinate Kyon Reagan in order to impress Haruhi Foster, but Nancy Nagato stops the attempt and eliminates Ryoko.
Once that's over with, in Melancholy 6 the villain unleashes her strongest threat against the world to date, but Kyon with the aid of the Scooby Gang manage to thwart the villain, with a kiss, no less.
OK, then there are episodes where the Good Guys go on excursions to baseball games and deserted islands, play computer games, and join rock bands with the villain. Not exactly your usual Scooby Gang vs. Villain interactions, but I did say things would be strange.
So there are problems like lack of evil intent, and hanging out with the villain everyday in the clubhouse is weird too. But I think we could open new vistas in The Analysis of Haruhi Suzumiya with this bold new interpretation...