The bosses have a character ? Do you even hear them talk outside cutscenes ? They are a svastika away from the stereotypical bad guys.
If you look at it like this, of course the games are going to be similar, but maybe you need to look deeper.
You don't have a brother, as far as I know, your parents weren't horribly murdered.
Jock vs Faridah, she is actually a well developed character.
You have a past and future instead of being a blank slate.
Deus Ex bad guys were actually really well developed characters with backstories, strengths and weaknesses.
If infiltrating a docked tanker and blowing it up is the same as smuggling yourself onto a ship headed to nowhere then we are probably playing different games.
No Paris catacombs.
Pritchard is actually interesting person to talk to.
Taggart, Sandoval and augmented people going crazy are themes not present in the original game.
I agree that HR can't offer the same level of depth like the original, to say that they shamelessly ripped off the story and locations is a bit naive, they gave a few parts a lot of attention, while skimping on others, which, in my opinion, resulted in a better game. Maybe it's not as much fun to explore every single nook and cranny and you don't have that much freedom, but the game plays much better. Fuck, you can just run straight for the top level of statue of liberty in the original and ignore the whole level ...