If we're honest with ourselves this is... quite a bit better than Shock 2. And I really do love System Shock 2. I'll try to explain why:
I think it's rather different than SS2, despite all the comparisons. SS2 is first and foremost a survival horror game about resource management, and in many ways has more in common with the likes of Resident Evil than Thief or Deus Ex. In SS2, developing your character generally either gives you more resources (get hacking -> more stuff from hacked containers; get maintenance -> save inventory space on additional weapons, etc) or makes you use existing ones more efficiently. The game is very deliberately built around this idea, and the oppressive atmosphere and claustrophobic level design (very different from Prey, which has a lot of open space) add to the feeling of just barely getting by (until you become packrat god anyway).
Prey, on the other hand, is more about exploration. Resource management is much more forgiving, even on Nightmare, it's much easier to just avoid combat completely, and your abilities are often used to gate your progress through the world in various ways, rather than making you more robust per se - the overall world design is almost Metroid-like in that sense. You do get a lot of alternative ways of dealing with situations, but crucially, these are often not based on your character's abilities, but rather your own clever use of available resources (so for example, most Leverage barriers can be removed via Recycler Charges, or just blown away with a gas tank). The end result is much more sandboxy, although it's still a relatively strict sandbox (hence reviewers whining that they couldn't play it like Fallout 4).
1) The weapons actually feel good and not clunky / almost all weapons in SS2 are a bit wonky.
2) There's nice environmental interactions that were not possible in SS2.
3) There is quite a bit less hand-holding than SS2. There's no intrusive tutorial and the station opens up in a way SS2 never. I am at a point where I can literally go anywhere I please - and get my ass kicked because it's quite hard.
4) The inventory system is less of a pain.
True, though I'd say the inventory system is too forgiving. Things stack too much and you get way too much inventory space from suit upgrades.
6) The skill tree is a bit better balanced than in SS2 (which had many borderline useless abilities)
It's better balanced, but much worse at letting you actually define your character and producing varied builds. As it stands, you get so many Neuromods, that you can basically max out 3 out of 6 trees. It also has too much low-hanging fruit, leading to way too many mandatory picks - why wouldn't you get everything that costs 1 Mod, the value is simply insane on those. SS2 in comparison, made it prohibitively expensive to get new skills - the first level was 10 modules, and the following ones were much cheaper. This led to less experimentation for the player, but more distinct builds and choices mattering more.
7) There is more freedom in solving puzzles / rooms. There are more options than in System Shock 2 in general: vent, move the obstruction, blow the obstruction away, fight through alternate route, find password, hack, repair, turn into a coffee cup, shoot a button with your nerf gun... that's not even all of them.
Yes, but this isn't really even something SS2 tries to do, imo. It's more like a proper RPG, where if you have Hacking, you use Hacking to solve your problems whenever you can; and if the same problem can be solved by a dude without any skills hitting a button with a nerf gun, then that devalues your investment in Hacking.
2) The audio logs in SS2 are, while campy, more interesting as a whole
They're more interesting in and out of themselves, but overall, Prey's audiologs, emails, and environmental cues (the post-it note room in Psychotronics was such a cool idea) do a better job of selling Talos 1 as a real place where real people lived and worked, rather than just a series of game levels. Close to the end, I actually found myself feeling a bit sad every time I found a new body of a crew member, which I think speaks to the strength of the worldbuilding.
4) The enemies are more interesting/varied/memorable.
They are conceptually and visually more interesting and varied, but enemies in Prey win in terms of gameplay. They actually require different tactics and approaches to fight effectively that go beyond just picking the right weapon and ammo type.
6) Maybe I am the only one but I like that enemies in SS2 respawn. Keeps you on your toes and drains your ammo
They respawn in Prey as well. There are ambient respawns which happen when you leave the area (I think), and also scripted respawns based on main story progression.
On that note, Talos 1 in Prey is a much more dynamic environment in general, and it changes based on events in both the main plot and side quests. I don't know how far you are into the game, and I don't want to spoil some of the cool surprises, but let's just say areas that you've already visited can become dangerous in ways other than just new enemy spawns.
7) I find OS upgrades more meaningful than the mod chips
Yeah, the chips overall were pretty boring, and the immortality chip is hilariously overpowered.
9) No fucking EVA sections; Jesus those suck
I loved those, actually. Just being able to go out into space and travel between airlocks (and the station actually making sense topologically both outside and inside) was really awesome. And from a gameplay perspective, I loved how the suit made you much more vulnerable, and how exposed you constantly felt in it. Enemies like the Weaver with their hit-and-run AI seem almost designed for microgravity, and are relatively harmless otherwise.