What bothers me about Deus Ex Human Revolution is that the game designers unrealistically gave Purity First and their sympathizers purely secular justifications for their beliefs. This is highly unrealistic. There is little doubt that in real life, the vast majority of Purity First and their ilk would be religious fundamentalists. They would use religious fundamentalist justifications for their anti augmentation beliefs.
Of course nobody wants to tackle religious fundamentalism in a game. But imagine if someone had the guts to do so in a game? Now that would be the makings of a spectacularly memorable game.