The hubs weren't too bad. I think that both Detroit and Hengsha were pretty fleshed in, and felt pretty lively.
My biggest complaint was that the central high-brow concept they pushed--"is augmented man not man", "are we playing god", et al.--was just woefully underexecuted. I felt more empathy for poor Gunther in the first Deus Ex worried about being phased out than I did for anyone with or without augs in DX:HR.
As presented, for example, augs were strictly the better option if you could afford them. 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.
Even the gameplay and combat itself didn't support this--there was no real "Oh no, they've got augs, ruh roh" to speak of, except maybe the boss fights. In the first game, for example, you go up against a fellow with augs as blinged out as yours, and it really really shows. The somewhat augmented humans are a bit harder to fight.
However, in this one, augmented humans or not can all be effectively one-shotted during stealth. There's no real feeling of "Oh, watch out, some of these troops are notably better"--contrast with, say, how in Dishonored or Bioshock you could run into enemies with similar abilities to yours.
And the ending...oy vey.