I've come around on Prey (though the complete stagnation in weapon/enemy variety and level design after the Arboretum still irks me to no end), but SS2 is still the deeper, more intricate game
It has been a while since i played System Shock 2 (which was when i played the Prey demo back when it was released but couldn't buy the game, so i played through SS2 to cope), however personally i find Prey to be the better immersive sim overall (and in fact i consider it my favorite immersive sim so far). The main reason is that Prey has overall more mechanics to play around with and the levels are designed to let you take advantage of all mechanics to allow you play with in variety of different ways (these three are for me the most important aspects in an immersive sim). I never got that feeling from SS2.
(though i agree fully with the enemy variety, Prey has very bland enemy designs - mimics are initially interesting but every other enemy is basically a mimic with a different behavior)
The various threats of the Von Braun more meaningfully impinge on your resources than the worst Talos 1 has to offer. Hoard all you want, but you will at some point find yourself low on medkits, bullets, or psi hypos and have to adapt
While Prey has more stuff around (and recycling makes it possible to use pretty much everything :-P though i guess you can do the same indirectly in SS2 too via the Recycler, but that happens later in the game), the only time i remember getting low on resources on SS2 was in the latter part of the game where you cannot backtrack and there are no spawns that give random items. Otherwise when playing SS2 you can pretty much wrench your way through most of the common encounters which allow you to both save ammo and pick up random stuff from the corpses (a strategy that also works in SS1 - i never ran out of medkits for example). Medkits and such are also mainly useful until you find the resurrection pad, after that it is often more convenient (and resource saving) to just die (technically there is a nanite cost but i practically forget it is there, i do not remember ever running out of nanites in the game).
Managing your character build is essential in SS2 where in Prey you can pretty much pick whatever you want (or nothing at all, per the requirement that "No Needles" be accessible to achievement hunters). Character upgrades are as vital and rare as your other resources
This isn't something that has happened on my playthroughs of SS2, but i've heard that in SS2 you can end up with "impossible" builds at the late game, which can be a big PITA.
SS2's mix of hand-crafted encounters and random spawns are designed to catch you off guard in tense moments. Prey has an interesting ecological development as you progress through the campaign and return to previous areas, but all spawns are scripted and enemies typically patrol a single hub
AFAIK Prey enemies also respawn even if you do not move on with the story, but it takes a while and they only respawn if you enter an area (ie. they wont spawn nearby). It'd be neat if they respawned like in SS2 though since i'd have more stuff to throw in the recyclers :-P.
The moans, clanks, and clatters of enemies are both spine-chilling
Yeah, SS2 excels here. Hearing the monkeys scream always make me stop (after my first encounter with them years ago where i died on the spot :-P) and all i manage to think between "That's the tri-optimum way!" and the sound of servos moving towards my direction is "fuck", often followed by an explosion :-P
Prey unfortunately inherits the awful mixing and nonexistent directional sound of most contemporaries
Yeah, it doesn't seem to have any form of proper sound propagation - the sound direction for enemies always comes directly from their real position instead of taking walls and openings into account. On the other hand there are several audio (and visual) cues about enemy state and position, so this isn't much of an issue.
(Also FWIW there are other immersive sims nowadays that use advanced sound propagation, for example Deus Ex Mankind Divided has a rather advanced sound engine)
Since the player wakes up on the Von Braun a month after everything goes FUBAR, audio logs are able to chronicle the catastrophe and build intrigue, where the logs on Talos 1 can only establish last week's office conflicts. Plus the story twists and turns are flat out more engaging in SS2
Yeah in general i'd say that i found the story and writing more interesting in System Shock 2.
