Oh, I don't really like Bioshock either, but of all the immersive sim games I've played, Prey has the most in common with that one. In terms of setting and premise it's much closer to System Shock to be sure, but the horror and storytelling elements of the SS games make them feel different. Bioshock is a horror game for about 20 minutes, and the scariest thing in Prey is a touch screen.
Some similarities, though many lifted from SS2 by Bioshock:
Intentionally misleading introduction with aerial travel, using a camera to research enemies introduced about a third of the way through the game, moral choices that don't really end up meaning anything, hacking turrets with an annoying minigame, powering up with injections, scampering enemies, clumsy gunplay, a radio guide with an ambiguous identity, a main character with a similar issue. But it might be more of a feeling thing, the FOV, the art direction, the gameplay. It's certainly more Bioshock than it is Arx Fatalis, grant me that.
Prey has more interesting tools and a world better designed around a the implementation of these tools. You feel clever when you drop an apple and turn into it to get through a broken door or use a foam dart to hit a switch. It's a cool trick, but it feels less cool doing it for the 5th time and finding a keycard to the room a half hour later.