That's not really AI though, more to do with enemy placement and patrol routes. The AI starts when they detect you and the flushing out part wasn't any more intelligent then other games. Simply lay low until they settle back into their routines, who cares your buddy just disappeared 1 minute ago. And it was too easy to pick them off one by one after they start searching, coming around the corner one by one.
Yeah that is the problem with pretty much all stealth games really ... but maybe it is not a problem at all, but rather just a effective strategy. I would like to see more permanent consequences for being caught in a stealth game. This should be done in such a way, however, that the player doesn't become frustrated and decides to simply go back to save point or restart a level.
Maybe, you could have guards take unpredictable routes when they have been alerted once ... in pretty much all stealth games guards never usually follow you into vents/tough to reach spaces, but maybe there is a chance (as in they will not always do it) they will explore vents or flood the vents with gas or something when they have gone to high alert. Maybe they switch to heavier weapons when a threat after one of their buddies is taken out. You could have guards lockdown certain doors or sections of a level which had offered a short cut to a goal prior to the lockdown. These are just some ideas, but, like I said, they need to be implemented in such a way that they add value to the experience rather than simply make the whole thing frustrating and annoying.
Getting back to Deus Ex HR, the AI may not have been perfect, but they aren't total idiots either. Their ability to see/detect you felt realistic, and they are very good shots with high damage weapons that down you in a few hits on the highest difficulty (which made getting caught something you really didn't want to happen ... kind of like in the Thief series).
Like you said, future stealth games (and games in general) need to find a way around the slow and steady approach of the player where you can just pick off otherwise difficult enemies one by one as their buddies get alerted for a few minutes and then proceed to go on like nothing happened rinse/repeat. You can do this in most stealth games and even most FPS campaigns.