Here's what I've done, in short, with the levels:
Gameplay:
-Balancing of paths. Sometimes in Deus Ex there was an optimal path to take no matter the build.
-More locked doors. Primarily to give lockpick skill more weight that it needed.
-Bug fixes.
-AI improvements. Half of the AI improvements in GMDX are done via the maps, which is good because some things are situational. Some AI react to stealing, more AI react to breaking and entering and so on.
-Swimming related. These are always minor changes to give swimming skill and aqualung aug more weight, for example in Everret's fish tank I made getting to the goodies and back harder to navigate, but it's still the same old fish tank. Very minor and simple changes that make the related RPG systems that much better.
-More challenges: this would just be an extra camera, NSF, turret, greasel or what have you were it makes sense to do so.
-Environmental hazards: There were plenty environmental hazards in DX that you could simply turn on regen aug or speed enhancement and run right through. Hazmat suits and the environmental training skill were not necessary. Again minor changes help with this, and the God-like regen aug has been nerfed significantly.
-Expansions: usually these are just to give more weight to the lesser portion of the RPG systems (again). So I'd add an extra room here and there that is locked with a door/keypad.
-Refreshed keycodes: This is simply for anti-exploitation. The keycodes that cannot be found in-game by any legitimate means have a new number combination so players cannot look up the codes and cheat.
-Events. Example: in the trailer @00:50 you can see a helicopter taking off. This was simply to remove a non-interactive object with an unrealistic collision cylinder from the game world. Before we could walk right up to it, fire rockets at it and so on, but it was in no way interactive when any player would realistically expect to be able to.
-Additional enemy-placed proximity mines. Gives the demolition skill more weight.
-Ammo redistribution: This was done primarily via code (for example a box of pistol ammo gives you 4 10mm bullets rather than 6), but sometimes ammo/tools are removed to make the gameplay more strategic and challenging, or at times ammo is added to make picking a locked door worth the rewards in the rare instances this happened.
-Less explosive barrels/crates. These were free ticket to opening locked doors or blowing up robots etc. They are also exceptionally useful if you take the new and improved microfibral muscle aug as you can throw stuff around at super strength.
Where there would be four TNT crates there are now two for example. Just for balancing and challenge.
Visual:
-Additional decorative detail. Skirting boards, power outlets, shipping crates, plumbing (pipes), ventilation and so on. Usually minor out of the way details that in no way effect gameplay that simply help Deus Ex's boxy and at times bland (bland visually) level design look more detailed and realistic.
-Texture alignments.
-Improvements to skyboxes.
-Some NPC types have more varied faces. Hong Kong Military police for example, some actually look Chinese now. Three facial variations as opposed to 1. UNATCO HQ as another example, the guys working in the offices do not have their face masks and helmets on. Only visible if you disable HDTP character models though.
-Additional details based on the real world. For example, just as Liberty Island and other maps were loosely based on the real world location, I've took the time to study images, watch virtual tours etc to add more real world details to certain maps, though obviously with Deus Ex's setting and events taken into account. So for example in Liberty Island's pedestal entrance I've made the Torch monument more true to real life, added two pillars, spherical lamps on the wall, a desk and so on. Just minor details that make the place look better, more detailed and more simulated.
Overall as you can see the changes are primarily gameplay related, because I am gameplay mad. I'm not a "storyfag" or graphics whore, though obviously graphics and story are still very important.