Because there's nothing to say about any of these, it's done better in other games.
Get updated bot. You're behind your programming.
What does it do that no other game does?
Crafting? Already done in many other games
Elements reactivity? Already done in other games
Powers? Already done
Immersion into a space station? Already done
Metroidvania level-design? already done
The game is a big déjà-vu.
Prey has so much going on creatively it actually loops back around to undermining itself with too much choice.
I know that sounds like a meme but it's true.
It's like the developers were like "we need people to be able to HACK into rooms! oh oh, and leverage! Oh but what if we also added a nerf gun! Oh and we should also add some walls to gloo-climb. Oh oh, what if they could also recycle the door!"
It feels like they were going for the Deus Ex "multiple approaches to problems" style of gameplay. But in Deus Ex, you get multiple distinct skills with distinct options (lockpicking is generally good for acquiring items and opening back doors, electronics is generally good for disabling security systems, with some overlap between the two). Deus Ex is not afraid of outright blocking you out of non-critical areas or making things WAY harder if you don't have the tools for the job. If your lockpicking is good enough, you can outright bypass the entire NSF warehouse return mission and grab the datacube you need instantly.
Prey on the other hand, will add super small areas (in some cases one ROOM), and then add 5 different ways to access it. In theory this is cool, because players get to utilise their skills. But it ends up resulting in virtually identical gameplay. If I hack the door, I enter the room and pick up the items. If I use leverage to move the crates blocking the ventillation shaft to enter the room, I enter the room and pick up the items. If I nerf gun the button next to the door, I enter the room and pick up the items. There's virtually no discernable difference between builds, and the skills will more often than not undermine themselves because you can just pick 1 of them and ignore the rest, since they all access mostly the same areas anyway, and wherever you can't access with the right skills you should be able to nerf gun or recycle your way into.
It is as if someone took the core ideas from previous immersive sims, only understood the surface level concept of "more player choice == good", and then copy-pasted it everywhere around the station.
The problem isn't Prey's lack of gameplay, it has far too much gameplay with far too little depth to really be compelling, resulting in a sort of "imsim soup" where it has all the elements of a good imsim and they all function correctly, but they are mostly consequenceless.
But your logic sucks anyway. It's reductive to the point of being absurd. Everything has been done before, and I can use your same logic to basically refute any games quality, even classics. For example:
What does System Shock do exactly?
Wire puzzles? Many games of the time and before contained far more complex, interesting puzzle mechanics already.
Combat? The combat in system shock is clunky and horrible. It came out the year AFTER doom and it's combat is a step backwards in every possible way.
Respawning enemies? Already done in countless games, including Ultima Underworld, it's clear inspiration and on the same engine.
Cyberware and a cyber inferface? That's just a clunky mouse-driven HUD, which pretty much every first-person PC game of the time had. Again, look at Ultima Underworld, it's direct predecessor, which has a very similar interface in many ways.
Metroidvania gameplay and selectable gadgets? Plenty of other games already had this.
