'Flare: I haven't been making a list, and my memory is sometimes lame. So I'll list what I can remember:
Range weapon mods affect projectile weapons.
Laser weapon mods no longer 100% your accuracy, but instead give you half your standing accuracy bonus, and make the other half add up twice as fast.
Using a scope no longer makes your shots 100% accurate, each weapon has it's own scope accuracy multiplier (putting a scope on a pistol isn't going to magically make the pistol a sniper rifle anymore).
Putting a scope on a weapon no longer reduces its non-scope accuracy.
Crouching with a rifle or heavy weapon makes your standing accuracy bonus timer increase a bit faster, reduces recoil slightly, and reduces scope waver.
Each shot fired reduces your standing timer a bit (only really relevant with rapid weapons).
Crouching/standing or zooming/unzooming reduce your standing timer.
Crouching into a fall reduces damage taken.
HL-style duck-jumps can be performed.
Jumping while coming out of a crouch increases your jump height slightly (not really noticable normally, but with the speed aug you get some real height increases this way).
Scrambler grenades have been replaced with holographic decoys.
Lasers are invisible unless using IR goggles or the vision aug, which both have new effects.
Laser bug involving throwing a decoration (crates, etc.) into their beam fixed.
Combat strength aug replaced with electrostatic discharge.
EMP and energy shield augs have been merged, old energy shield replaced with a concussive blast aug.
Aug energy use reworked.
PS20 replaced with flare gun, made stackable.
Some new features with decorations implemented.
Hacking skill modified to give you new abilities with each new level, rather than simple hack speed and time improvements.
Low tech weapon skill now increase your rate of attack, as the description says it should.
Low tech weapons are slower when used underwater (fluid resistence).
More gibs when exploding people.
Some fragments (pieces of wood when braking crates, shell casings, etc.) persist indefinitely.
DTS takes up only one space, and does less than half the damage it used to (which is still a lot of damage).
A few weapons are shiny in first person (without simply making them bMeshEnviroMap and sacrificing all their texture detail).
Flare darts replaced with weak EMP darts.
Mini-crossbow has shows correct darts loaded on the first person view mesh (this includes being empty).
Pistol can have silencer weapon mod, stealth pistol can't have laser weapon mod, but can shoot underwater.
Augmentation cannisters containing an aug you already own can be used to upgrade that aug.
Repairbots and medbots only restore a set amount of energy/health.
Progress bars are now a blue to red progression, unless describing health, in which case they're still green to red.
Weapon draw/holster speed bonus with weapon skill (double bonus for low tech draw speeds).
Misc. oversights in original code fixed.
Umm... I think that might be it, but I could be forgetting some stuff.
Postal: messing with RenderOverlays(). Actually, no, messing with CalcDrawOffset(), which is called by RenderOverlays().