> There wasn't any downside to piling them on, nobody in the game gave two shits whether or not you were man or machine. No quests really changed if you were really chopped up. It just felt phoned in and handwaved.

I agree with the rest of your post, but this was pretty much explained by saying that ALL the augs Jensen has are already installed in him at the beginning of the game. Them being unlocked as the game goes on had more to do with Jensen getting used to controlling them (as opposed to having them installed and being able to use them then and there).