So I managed to play the game about a month before you did, and I have to say I pretty much agree with everything you said.
I had the game for a year before finally deciding to play it, I honestly didn't know what to expect, just that it always seemed to be a bit of a 'darling' on Resetera and a few other places, so I picked it up.
Well... Once I got out of my apartment, which was an amazing reveal! I'm so happy that wasn't spoilt for me! I... Really started to find myself becoming a bit bored, I don't know why but it just wasn't 'clicking' with me, but then slowly everything started to fall into place.
Aside from the truly science fiction atmosphere, you begin to see just how well they designed the environments, it really is a game that you can just spend hours exploring in because once you find a new route you end up going down a rabbit hole discovering new hidden rooms and more bits of the story.
The big comparison is to Bioshock 1 and System Shock 2, but Prey feels different in many ways, the big one as mentioned is how if you clear an area of enemies, over time they'll re-spawn but will have changed slightly.
Oh and I loved how as the infestation began to damage more parts of the space station this has implications on some parts of it which you can choose to fix or even prevent! Though it did kick me in the teeth when I entered that room full of gas and couldn't use my guns!
The main problem the game has is once you start to find NPC's, they're... not well done, aside from the fact they often talk over each other, they're so lifeless, when you find that stronghold in the cargo bay, it really does illustrate how little thought went into them, then if you get both the doctor and the lady in your office... when you talk to them... Good god it's bad.
But the biggest thing for me that I started to love was how so many 'locked' rooms became a puzzle to try and figure out a way in. There was just so many ways to gain access to some rooms they felt like their own miniature puzzles. When you finally get access it was a huge moment of euphoria. Even if there's not much inside the locked room, when you figure out a way inside you're so excited.
I uploaded a video today exploring about every locked room in the game is a puzzle and how the game educates the player so subtly, which can probably explain what I mean by the puzzle rooms better than this post can.
But the main thing, Prey just feels like the first truly science fiction game for years, you really do feel like you're on a space station in the future, they really nailed the world building with this one.
Just... Play Prey!