Heiss from Radiant Historia, a very underrated NDS RPG. So many of the plot's twists and turns are caused by him as you try to return the world to its correct history....only to realize at the end that you are always on the palms of his hands.
Personally recommend that game. Its battle system is unique; not your usual turn-based grinding. Time-travelling can get heavy but the dialogue almost always entertains the player, especially the side-characters. This is one of those games where if you make the wrong choice at a critical juncture you'll have to restart at that juncture so I recommend a FAQ if you are pressed for time/make full use of your game time. Main character may appear to be the typical stoic hero but there is a background to his origin and who he truly is as you progress further (he's not a Cloud; no subconscious implantation of fake memories here).
Vergil from Devil may Cry 3- As a villain he was great, as he was a grey character. He also meant a great deal to Dante and was hyped constantly during the game, and never disappointed. Plus his final words with his final fight just sound so epic.
Meruem, Chimera Ant King from hunter x hunter. He's just an overall great character let alone villain.
Meruem, Chimera Ant King from hunter x hunter. He's just an overall great character let alone villain.