Don't get me wrong, if you can encourage someone to achieve those goals through a story then you have a winner. Like Half Life.
Those are the types of stories that blend well with the Shooter aspect. Sometimes games put too much faith in a massive backstory intent on futilely serving some higher purpose. One that makes only passing hints at or is totally disengaged to the whys and hows of a player's actions. Cases in point, Unreal 2, Halo, Max Payne. Certainly some of these stories are worth persuing for their own good (Hence the novelizations), but most players can probably set them aside while they blow stuff up if not ignore them totally.
While a good storywriter can add a layer of depth to the world and the characters of a developer's bland narrative, I think their main purpose should be more of structure than of form. They should make sure that the pacing of the game is just right, that tension builds up to a climactic event for example. The player should also know at all times why he is doing what and what higher purpose it will serve. A verbose cutscene explanation shouldn't be necessary if they can pull it off interactively through character scripting and level design. This integration of story and gameplay is what I believe the top FPS devs are aiming for.
"Nothing livens up a robotic hymn of doom more than an amazing pair of jugs." - Brak