Prey is one of those games that should be great; in fact it should be awesome, but for me it just falls short.
I can't be the only person who thinks that all games made with the Doom 3 graphics engine look exactly the same, and for my money not that good either. Admittedly Quake Wars is looking set to change this with a bang, as that looks amazing.
But anyway, back to Prey. After a great intro sequence involving our hero being rudely plucked from his local bar by aliens, we are dumped into an alien environment, and from there it's so-so FPS action all the way.
For me it's one of those games that never grabbed me or managed to get me interested in the story, which is a shame as I loved the premise, just not the execution. I found Quake 4 and Doom 3 similarly underwhelming, so perhaps if you enjoyed them this will be more up your alley. Maybe I'm just allergic to the Doom 3 engine!
For me the last great single player arcade shooter was Soldier of Fortune 2 (if you could stomach the violence!). More recently the best shooters have been multiplayer affairs or take the more strategic approach. For the former, Battlefield2 is fantastic (Battlefield 2142 is not so good, despite being newer). In the case of strategic shooters, Rainbow 6: Vegas is excellent, although heavy on the resources (just don't get Rainbow 6: Lockdown as it's abysmal!). Alternatively, SWAT4 is a very good game.
I hope my thoughts have been helpful!