Dark Engine melee is considerably more developed than in Deus Ex. In the former, the player's attack swings are actually simulated to collide with enemy models for damage or indeed to be blocked by the enemy's melee weapon (this is obvious in Thief but works in System Shock 2, even monkeys can block wrench strikes if both attack at the same time). In SS2 there's a more interesting dance to charging up a wrench strike, releasing it as you approach the enemy, and then backing away as soon as it connects. If you miss, the timing can be extended by rotating your aim so that the tail end of the wrench swing collides with your target. Thief has some more player mechanics at work for melee (blocking, right-to-left swings if you aim to the right side of the enemy) but enemy attack motions are pretty bullshit and not meant to be fought fairly, especially not versus a crowd. Meanwhile, Deus Ex melee just projects a hitscan check at the player's crosshair at a specific frame in the attack animation to see if there's an enemy in range (which has nothing to do with the actual weapon model). Attack animations are also randomized with slightly different timing for each so it's really just a spamfest once you're in range. To make things worse, Deus Ex hands the player a 100 damage laser sword (for reference, the crowbar does 6 and the sniper rifle does 25) halfway through the game, capable of oneshotting most enemies with no skill or aug investment and thus spitting in the face of melee builds. SS2 lets you become overpowered with melee too, but it takes some investment.
Deus Ex's ballistic simulation is more advanced than SS2's, but at the same time less robust due to some terrible implementation. I don't mean the accuracy system that requires you to stand still to stabilize your aim at low weapons skill, that's actually decent. I mean the wonky recoil that can take a full second to reset, hitscan accuracy tied to max range so the sniper rifle is pinpoint accurate at untrained skill, fake bullet drop for hitscan but only when you would have hit your target so you can't adjust for it by aiming higher, projectile range affecting only the distance at which shots start to drop off rather than their speed, a bug that makes the laser mod do nothing on scoped weapons, restrictions on the scope state that prevent a transition while you're in a firing anim, incomplete effects and poor sound design, lack of player feedback for hit registration, or a whole host of balance issues related to weapon types, skills, and mods. All of these have been meticulously addressed and overhauled in GMDX + vRSD. SS2's gun combat is rather more basic, but gets the job done with simulated projectiles for everything (even bullets), functional recoil, punchy sound effects tied to ammo type and firing mode, and hit sounds and health bars that clearly indicate the player's shot connecting. There are balance problems and the weapon modding system is super boring, but SS2's combat has more solid foundations for a first person shooter even if it's less ambitious in the firearms department.
[Don't get me wrong, DX is still a fantastic game, but as a sum of its parts, mostly down to the level design and the freedom afforded by the systems]
