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I would have liked to keep the eyes though, very sharingan-ee. Oh well, since I'm bad, I can't have anything I want. Naturally.
Anyway, the whole explanation for the scars is absolute fail. Somehow "negative thinking" slows the healing process, for some retarded reason. Even if that was acceptable, it still doesn't make any sense. If you're a bad guy, doing bad things makes you happy, therefore its "positive". Unless one of the side effects of the Lazarus Project was giving your body a conscience that gets miffed when you punch people in the face, that's just dumb. You know your reasoning sucks when "because of the dark side" is a better explanation. :/
They should just have made the cosmetics optional, or left them out altogether.
Negative emotion can be bad for someone's health. Studies done on laughter and sick people etc... Just import a save, you get a huge boost of resources. Or beat the game with Paragon first. Beating game = more resources at the start of a new game. You can start with 50k of each.