Really? It's unbelievable that people would be antsy about this? Outside of "terking our jerbs" (I don't see a job that wouldn't benefit from augmentations in some form) and being just plain better than a non-augmented human, there's also the "it's against nature/God" argument. You want to tell me people aren't convinced by that "argument"? Just look irl at the abortion debate, the non-straights, "GMOs", some anti-science arguments, etc. Widespread augmentations like in Human Revolution are much more prominent and non-abstract, so people who are gullible enough to fall for that argument are going to have their panties in a twist a lot more fervently. If you retort with "but it's not logical", that's not the point, none of these things are logical and humans don't always operate based on logic alone.
Human Revolution's narrative problem is that it doesn't deal with the actual problems it brings up - withholding of knowledge, glamorization of news personalities, healthcare, and the dissemination of media. I'd say transhumanism too, the game might pretend it has some debate on the matter, but in reality it has 2 feet firmly placed in the pro-augmentation camp due to Jensen being able to solve all the problems he encounters while being augmented, even against his will. There is no doubt that Jensen is better at everything he does after he gets augmented, we feel that in the gameplay too. We start out with zero augments, being only vaguely aware where our enemies are, and getting gutted by a guy with augments, to being able to see where our opponents are at every step, being able to regenerate health, and knocking out people with a punch to the face (you can't do that before you get augmented, I tried). And that's only our starting get-up.
It also doesn't have much to do with the original Deus Ex tbh, the events of this game don't gel well with it, especially with how slick and non-obtrusive augmentations look, while looking like a freak with metal prosthetics was a huge deal for at least Gunther in the original.