Underappreciated in every sense. Some points I think are not covered by others. I feel bad for the developers...
Production:
I, like many others, do not understand why this game is so underappreciated. I'm a designer, programmer and did quite a few multimedia work. What I can say is that this game screams production value. There are tons of "money shots" where tons of man-hours are spent just for a particular scene, I think those are worth the price of admission. In almost all aspects of the game, there seems to be details everywhere! Details that are so well crafted to the context of the game's environment. The sound is rich, the design is top notch and music that combines a scene gracefully. All that combined together in a seamless fashion that make sense. Prey truly immerses a player with it's atmosphere, since when was the last time a game has such a well defined and researched theme?
Gameplay:
Some people believe that the portal and gravity system is all hype and that it does not provide any real evolution of gameplay in the FPS genre. I enjoyed Prey's gameplay and it never made me feel like I'm blasting armies of clones in endless corridors like in many other FPS. The fact enemies can appear in multiple surface gives a whole new definition in FPS gameplay. I always wonder when I can shoot enemies from all sides of the screen rather than just an X-AXIS gameplay...
I believe that if the developers omitted the "death-walk" sequence and use the traditional "gameover" system, less people would complain about how easy the game is. For me, the game is not very easy but that system empowers me way too much that sometimes I don't care about Tommy dying or not to save myself some ammo instead of mindless shootings as a last resort save-your-own-ass solution.
Polish:
It feels like they tested the game thoroughly and fixed tons of bugs before it shipped. Games that introduce new gameplay elements, like the gravity shifts, usually are far from perfect coding wise... I enjoyed the smoothness and the console-game like rigidness that Prey is. No patch is yet required for PC users like me. Even in multiplayer, I feel a polish-ness that not much other multiplayer games offered. I'm certain that the developers optimized the network source of the Doom 3 engine. The most surprisingly of all is that I can run Prey better than Doom 3 in my almost obsolete Athlon XP 2600 and ATI 9800. It was very playable on medium settings with screen resolution of 1280 x 1024.
Unique:
At first, I was a little turned off by the "over-powered" sound and the "under-powered" performance of the rifle. But I learned to live with it especially as my arsenal grew. I like the design of the alien weapons albeit the familiarity of them all. Prey has one of the most well crafted alien guns I've seen in a game. My favorite is the secondary firing mode of the rocket launcher, extremely well executed. Another favorite is the "plasma" beam of the Leeching Gun, it feels just right "power vs sound vs reaction of the player backing up".
Also, the enemies are very imaginative also. The design is nice but I enjoyed the unique abilities of each enemy even more. I think my favorites are the "harvester", "keeper" and SPOILERRRRR "jen-modified". The harvester going in those organic teleporters are awesome. I disliked the design of two-legged hounds as it feels too generic for the standard set for all other high quality aliens. However, the glow in their eyes impressed me, finally a game that uses lighting right in the FINEST details.
Level Design:
Too linear you say? I don't recount where was the last time I played a FPS that is non-linear. The only non-linear games are those that simulate a world, like a flight-sim or city-sim or GTA (not by its linear mission, by its world). Yes, I do understand that the introduction of portals might lead some to believe a more dynamic flow of the player's progression. However, this is not the intention of the developers, they want to give players an extremely satisfying cinematic experience. With a non-linear gameplay, you might encounter random things that would destroy the intention and there is no true feeling of building up tension through progression (especially in the last portion of the game). However, I do think that if they have included a "portal" weapon of some sort that these complaints wouldn't be filed as much...
Conclusion:
For me, this has been the best FPS since HL2. And in some respects, I enjoyed Prey more than even HL2, especially the whole last few hours of the story.