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I wouldn't consider Metroid Prime or Portal to be FPS games because the overall structure of the games are different from other FPSes.

Portal at its core is a puzzle platform game, your "weapon" is only used to solve puzzles and it cannot directly actually harm enemies. The main purpose of the game is to solve puzzles and escape the facility.

Metroid Prime is more like Zelda in Space with guns, if you ask me. The overall structure is to explore the planet, collect items and artifacts or keys or whatever, solve puzzles and defeat bosses. Except for a few circumstances you are not required to kill most enemies and most enemies do not much require much strategy to actually defeat. Combat is mostly secondary to exploration, puzzle solving and item collecting. Samus in the games after collecting some powerups is an absolute beast compared to for example Master Chief in Halo, I do not think that anything in Metroid Prime can instantly kill Samus (except for Phazon overload in Prime 3) this is because the health system in Prime is built towards exploration while in Halo is build towards combat.

tl;dr Portal and Metroid Prime do not feel like other shooters to me so I wouldn't consider them to be FPS games.