In the alternate history of civ, however, every civ can be a villain civ. That's one of the strengths of the setting. I don't think it needs civs that are always good or always bad.
Usually, it's the one played by the human player that's clearly villain: breaking deals, surprise blitzkrieg, always taking more than giving, being hardcore intolerant religious fundamentalists, dominating foreign cultures, robbing/stealing/buying artifacts and great works, committing genocide in any conquered city (and replacing part of the population with your own culture citizens), adopting whatever government and policy that suits your goals and not the goals of your people, founding useless cities in the arctic/desert whose population always starves just to get resources, etc. But of course, as a player, you can fall for your own propaganda and tell yourself that you're doing all this for the good of the world, because once it's all yours everybody will be better off.
I can hardly imagine that an AI civ in a game is more evil than that, regardless of it being called Nazi Germany or Soviets. Admittedly, the AI also tuns out villainous at points, because their incapability to play the game leads to uproars and rebellions, but I don't think that's even close to the average civ player's villainy. Good thing most players (I assume) usually don't make the connection between their in-game choices and what that would actually mean in real life. Otherwise, we would all be psychopaths, right?
