More Fun To Compute
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I don't know what is the thing that this list ranks anyway...
It lists the best FPS games justified by their shooting mechanics or first person games in general?
Games like Metroid and System Shock 2 are much more than just FPS games. You can't compare the two with a Halo or a CoD game that are, basically, shooting galleries. I wouldn't even call Metroid or SS2 FPS games. They are more like adventures mixing shooting, exploration and RPG elements in first person perspective.
Since Bioshock and Metroid are so high up then I don't think that shooting mechanics are the main or only criteria. Probably the fanboys at IGN came up with some way of voting for their favourite games for fun instead of doing more boring work that generates less clicks.