The baron from Jak 2 wasn't single-mindedly evil. He was a ruthless despot to be sure, but he was trying to keep his city in order whilst holding off the metalheads. Dutch VanDer Linde from RDR had some depth, in that he did what he did in pursuit of a genuine vision, or at least an ideology. The real villains in that game were of course the government forces, and even they were doing what they thought necessary. To quote Edgar Ross, "Me and Fordham here, we're the bad guys, we enforce the rules, and while the rules may not be perfect, they're really not that bad, and while civilization may be boring, the alternative is hell."