Legacy of Kain: Blood Omen...you were the villain, and you had a very solid point.
KotoR; Kreia.....she makes the best point in the entire series. Jedi and Sith are too extreme and overzealous. True balance comes with being a grey jedi
Mass Effect; Saren. If we're following ME3's trash canon ending, then Saren was right, and it would've been better to try and save some races, instead of all of them just dying.
Mortal Kombat; Scorpion. He only wants revenge for being murdered by Sub Zero, after he kills him him vows to protect Sub's younger brother (MK2 Sub).
Assassin's Creed; Haytham Kenway; He wanted to unite both orders as he saw both were ruthless and willing to kill innocent people for pieces of Eden. We later find out that he was right in Rogue, wherein assassin's are pieces of shyt ultimately, and are no better than the templars.