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FFXII's Vayne, Cid and Venat had a damn fine line of reasoning. It was almost sad to see the way they ended up, like if you player was actually the villain. The same goes for Andrew Ryan. "A man chooses, a slave obeys", damn that line keeps sending me chills down my spine.
Zeus on God of War II/III was totally right in my opinion, trying to eliminate that prick Kratos and bring back order to things. Albert Wesker in RE5 too, like many already said. And Kerghan from Arcanum, with his nihilist/buddhist line of thought, his final speech was damn great. I miss that game. Seymour from FFX was pretty much like Kerghan with a lot less experience, so maybe I could put him here too.
While all of these I mentioned could still be considered anti-heroes, Kefka was a true villain with also a reasoning. While you really could understand his point, one would still desire to see him die a screaming, painful death. That's great too.
