Probably because most fps mechanics are pretty restrictive. I mean, a lot of shooters allow the player to do little more than run around and shoot. Meanwhile, something like Metroid Prime gives the player a strafe dodge to avoid projectiles, a double jump to avoid shockwave attacks, and a host of other tools which can be used to interact with bosses (grapple beam, visors). The behaviors of enemies and bosses are dependant on what the player is capable of. If the player can't do a whole lot, then enemies have to be neutered to compensate. An enemy with a fast projectile attack wouldn't work in Halo or Half-Life, for example, because the player has no mechanic with which to respond. In Metroid Prime, a well-timed strafe dodge would get the job done.
So basically, shooters need more diverse mechanics to enable more interesting enemies and bosses.