Vaan, Tidus from the final fantasys.
Raiden in metal gear solid 2 (although, this is more or less eliminated by him being cyborg ninja in 4)
But, the most unbadass character for me would have to be...Nowe from Drakengard 2. I mean, the first game you played as a phsychotic, pissed off, mute known as Caim that was just badass. And then, the second game replaced him with a whiny, little J-RPG type(before you kill me, i have nothing against J-RPG type characters. But, i hate when they try to throw it into a universe that it just simple doesn't fit with) ***** known as Nowe. He basically spends all his time whining as to whether what he is doing is right, vocalising every thought and basically just complaining about everything. So, you go from a protagonist that never said a word. With someone who just doesn't know when to shut the fuck up. Not saying i hate the game either, but lets be honest...NOBODY LIKES NOWE!