1) Increased randomized shop base prices by 100 (everything costs an additional 100). 
2) Any skill point reward over 300 now rewards 100 points less (nerfs most primary objective rewards slightly).
3) MJ12 commando melee attack knocks the player back more
4) MiBs throw grenades
5) MiBs and WiBs have a slightly larger blast radius when killed
6) Drawing any weapon now produces sound that alerts NPCs. It's only a small radius though, the Dragon's Tooth is louder (416 DTS, 224 all other weps).
7) All robot explosion radius when destroyed increased by 20%
8) Crouch-walking speed reduced by 15%
9) Player has no legs speed reduced by 10%
10) All grenadier NPCs throw grenades more frequently
11) Walker bots now have a flamethrower in addition to their standard machine gun
12) GEP-weilding enemies have 50% faster reload speed. 
13) Enemies weilding any other weapon have 20% faster reload speed
14) MJ12 and UNATCO troops have variable low chances to have their weapon replaced with a GEP gun, and additional chances to have lots or little ammo for it. 
15) MJ12 Commandos will occassionally enter a super speed state
16) Added more enemies across the game, mainly on hostile/action maps overlooked by previous versions, with extra emphasis on bots and greasels.
17) Greasel bites inflict poison (previously only the jump attack did, seemingly).
18) Gun Turrets will remain permanently active once triggered, unless hacked or multitooled. To aid against this great threat, turret confusion time when taking EMP damage is now doubled. 
19) Random grenade accuracy was already present from previous versions, however not that noticable; reduced base accuracy of all grenades.
20) Cameras now explode when destroyed instead of awkwardly shattering
21) Cameras now activate any nearby alarm units when destroyed.
22) Objects thrown with Micro. Muscle now deal 30% less damage to robots.
23) 15% chance nothing will be found in containers, up from 10%
24) Reduced random chance of finding GEP Rockets from containers.
25) Moderate to heavy EMP damage disables augs temporarily, duration scaling based on damage sustained (around 3 - 10 minutes). Note: doesn't apply to passive augs.
26) player damage recieved is increased by 5%, enemy damage recieved is reduced by 5%
27) any gep rockets found on a corpse will only give you 1