The amusing thing here is that looking back on it, very few of the villains really do anything. Post contains MAJOR DISSIDIA STORY SPOILERS!!!!

(SPOILER)Jecht and Golbez are typically working more for the heroes or their own personal motives (still good) than the villains so they are basically anti-heroes. Gabranth could probably be thrown in there as well despite only having a side story separate from the main plot.

Sephiroth is pretty much true neutral and actually doesn't do anything in the plot. He's got an interesting back story but one has to wonder why its a big deal he "figured out the truth" by killing himself when Mateus and Ultimecia figured it all out without having to do something so drastic. Sephiroth's actions are not even really evil as he basically helps Cloud and the other WoC by association achieve the goal of gaining the crystals and beating Chaos once and for all. His only goal was to end the cycle so he can go back and become a god in his own world.

Garland isn't really evil either, he's just trapped in a determinist mind set and is basically letting "fate" take its course. The closest he gets to manipulation is the fact he knows the truth about the Dissidia world and all its inhabitants.

Kuja is regretfully a pawn in this game as he is easily manipulated by both Ultimecia and Kefka to further their own ends. Kind of a waste if you ask me.

CoD is just a force of nature as usual and basically becomes Kefka's partner in crime.

Kefka spends his whole time trying to manipulate and control Terra and bring out her Esper form; as well as just causing general chaos for fun by manipulating Kuja. He's mostly a wild card causing trouble. He's actually one of the more active villains now that I think about it.

ExDeath is sorta just meandering around talking about the Void and doesn't really do anything, another waste of an opportunity.

Ultimecia and Mateus are probably the most active villains as they are the ones that formulated the plan to kill Cosmos and stop the cycle. They pretty much manipulate and use almost everyone on both sides.

Chaos is actually represented as a sympathetic character in the story and after reading the full set of Chaos and Cosmos reports, its pretty obvious that the real villains of Dissidia are the Lufenians of FFI as they are the assholes that sorta started this whole nonsense and drove Cid of the Lufenians insane who in turn created the Dissidia world and conflict to make Chaos go insane so he would achieve the goal of Ultimate Chaos (annihilation of all existence including the self). So yeah, I'm going with the Lufenians.