If I had to go with any sci-fi shooter game, that'd be X-Scape on DSiWare, mainly because of how engaging and unique it felt for $8. Metroid Prime is pretty awesome as well.
I've always had a preference to war FPS games (excluding most COD) over sci-fi FPS games like Halo.
No obvious choices? What if one of those games were someones favorite? Just because its a popular game doesn't mean they shouldn't be able to choose it.
I dream of a better tomorrow, where chickens can cross the road and not be questioned about their motives.