There aren't many good sci-fi shooters around (or sci-fi themed games, for that matter). Here are a few that come to mind, anyway:

UT99 / Unreal 1 (Probably too aged)
Alien Versus Predator 2 (Also kind of aged)
Gears of War (Never played it, but even the PC version has pretty good reviews)
Prey (GameSpot recommends this)
TimeShift (And this)
Lost Planet: Extreme Condition (Et tu, ludus)
Jedi Knight II: Jedi Outcast
Serious Sam

If desperation eventually renders you willing to accept a few RPG elements, you will most likely enjoy:

Deus Ex
System Shock 2

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Out of all the games listed so far, the Max Payne series and Deus Ex are my favorites. Did you enjoy any of the old-school SNES games, such as Chrono Trigger or Super Metroid? If so, I think there is a pretty good chance you've just been unfortunate to play the wrong, generic, post-2000 RPGs based on the Final Fantasy template. Not that I know what the "right" ones are. Possibly Mass Effect and Fallout 3, although I prefer the original Fallout games to the latter.

"Stephen Wolfram is the creator of Mathematica and is widely regarded as the most important innovator in scientific and technical computing today." - Stephen Wolfram