You're not messing up in any major or big way, it's just that your character either isn't psychologically accurate, or is psychologically accurate, but in a way that's creepy. As for playing a grey character, that's all right, it's just that Adam's 'greyness' is expressed through, well, how do I put it? A blind faith in his father and the US Gov't, and a refusal to acknowledge that there are flaws in need of fixing, or, alternatively, that he can fix them all by himself. As for not being generic, that's to be praised.

Look, the problem is that Adam is a person who, although he's grey himself, doesn't see shades of grey. He also isn't conscious about the implications of how he's been treated, even though he's supposed to be a genius. As mentioned, he thinks that being brainwashed into a killing machine is an ideal state, and, well, if you want him to not be generic, have him realize that it's not, it's unethical and he's been broken and reshaped into being a pawn. 

He doesn't have to see it right away, just gradually.