The level design is by far the best part, the levels are aesthetically consistent, impressive, and unique, and the layouts are intricate and facilitate exploration and effectiveness well. They're big without ever feeling empty, which is an excellent feat.
All of the system design tweaks and changes also worked really well, the new skill system was excellent (though Battle Training was still a bit more useless than I was hoping) and the perks were a pretty neat addition. Making the spy drone an item was a great improvement both in terms of the narrative and the gameplay, though I never made much use of it. The weapons were... well, I still suspect they were ripped out of a version of Counter-Strike, but either way they were nicely detailed, had excellent sounds, and most of all I loved the new implementation of recoil and how powerful it made the weapons feel, especially in combination with dust puffs where your bullets hit. Also loved the tweaks to the weapon mods.
Great economy, too - you actually really needed money in 2027, unlike... well unlike in any other Deus Ex mod I've ever played, as well as Deus Ex itself. Or Human Revolution, for that matter.
The only real let-down was the narrative. Really needed a proper intro to tell me who the hell I was playing as. Never really had enough time to get to know and care about the characters, so I never had any reason to like them or dislike them. The denouement in the end was cool, but it would've been cooler if I'd cared about what happened to any of the characters.
But I get the feeling the narrative wasn't a main focus during development, it seems the emphasis is primarily on the gameplay and especially the gunplay, and I can only applaud those priorities - it's a much more focused game than you expect from a Deus Ex mod, so what it does, it does really well. Completely worth the 11 hours of my life I spent playing it.