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I thought of a lot of characters in video games that have Pokémon counterparts, so I guess you could name them after them. Well, here we go!
Magnemite: Wheatley, Space, Rick, Craig, Anger, Morality, Cake, Curiosity
Chell- Oshawott, Dewott, Vulpix
GLaDOS: Roggenrola, Magneton
Uxie, Mesprit, and Azelf: Din, Nayru, and Farore (not necessarily in that order)
Yanmask: Majora, Skull Kid (when it evolves you can rename it Majora's Wrath)
Zelda: Vulpix, Gardevoir
Link: Golett, Riolu, Gallade, Pikachu
Peach: Gardevoir, Wigglytuff
That's all I've really thought of at the moment. You can submit your ideas if you want.