The following are my views on Prey and you shouldn't read them until you are done with the game:
Possible Spoilers:
Just finished Prey, and was quite good. I'd give it a score around the mid 80s. It lost its innovative appeal mid way through, as its unique aspects became less awe inspiring. Still what it did right was to keep things interesting through out. It wasn't a monotonous shoot em up, and I appreciated that. And while the storyline was a bit cheesy, it did involve you none the less. It made me care about the characters, which is something I can't say for just about every shooter I've played.
I was disappointed with the fact that the radio transmissions you hear from earth weren't fully fleshed out. I wanted to hear a lot more panic and widespread acceptance of an invasion. But that design decision made sense at the end of the game, when it turns out six months after the event the planet is still unsure of what happened.
I also like how they gave Tommy a military background. It is just a little thing, but helped connect the dots. I still can't figure out why Gordon Freeman, who is an award winning scientist, is also a genius with weapons.
In the end I'd say the game is quite excellent, but falls short of greatness. It wasn't an epic but I think the length was perfect for the ideas and gimmicks they had. While something like Half-Life 2 kept throwing interesting and exhilarating situations at you, there was only so much Prey could do. While the combat was good, on its own it wasn't that exhilarating. It was fun, but lacked the intensity of something like F.E.A.R. or even HL2.
The limitations of the Doom III engine meant you couldn't really have massive environments filled with all sorts of structures and enemies. They worked with what they had, and did an excellent job. However I think this is one of the last Doom III engine based games we will see. Even the boys at iD have admitted this and are working on a new engine. A Quake engine this was not.
While the ending leaves things open for a sequel, I think they firmly shut the door on any sort of an expansion.