I picked this up about 2 weeks ago, I'm now half-way through and 45 hours in (according to Steam), and I'm loving it. The first Deus Ex remains solidly in my top 5 best games, and this really wouldn't be all that far behind if I didn't still have the first on that list (and the only thing keeping the first game there over this is the much wider RPG elements and game complexity).
Two main gripes: had to reload an hour of playtime back because the game decided not to give me the Ghost bonus despite not altering anyone in one mission, and the bug that causes some enemies to die quite some time after being successfully knocked out has me worried for my Pacifist achievement. Lesser gripe would be that the aug trees aren't mutually-exclusive choices like the original, but rather a progressive path where you really can get everything if you have sufficient XP.
Also...boss fights are hilarious. I've been maximizing XP and therefore using takedowns over tranq headshots and stun gun, so I have a ton of ammo for both... and so far both bosses have been susceptible to the stun gun. As in, were killed by the stun gun. On the hardest difficulty. With no aug usage. In fact, so far the only thing my fully-upgraded pistol (the only lethal weapon I carry) has been used for is shooting open the odd wall that I'm too lazy to punch through.
Bots that turn hostile at EMP grenades tossed steathily behind them are also irritating, but don't seem to affect the Ghost/Smooth Op bonuses, so I haven't worried about that as much.
These are all nitpicks though. The game is frickin' fantastic.