There are enough good comments on Deus Ex, so I would bore you to praise the game again.
The issue here is why did people never mention about those SERIOUS flaws of Deus EX? That is the AI, note that I have the GOTY edition. Let me give you an example:
In the mission of locating info of plague virus in VersaLife labs, after addressing myself to the receptionist in the lobby, I hacked into the security room which was right next to the reception. The securities inside immediately shot at me and I returned fire, the scene ended up that all security personnels were wiped out on that floor but more surprisingly: the receptionist sat still and even spoke to me calmly as if nothing happened at all. Note that all fights occurred in the lobby and reception area.
So you get the picture, and there are a number of situations that you could find similar flaws or bugs. Deus Ex does have an excellent framework but its nonlinearity breaks down somewhere as you see in one example above.