My Top 5:

Persona
Obviously pokemon replace personas. The game would be staged in a non-pokemon reality and the bosses would be possessed by ultra-beasts corrupting their desires. Essentially, ultra-beast are what's causing pokemon to exist in the shadow world. The story could tie in "shadow pokemon" lore. The cast of protagonists include Red (you/student), Cynthia (your teacher), Roxie (classmate/punk girl), Lillie (classmate/shy girl), Elesa (classmate/popular girl), Wallace (classmate/Artsy Guy), and Z(Mysterious Guy). Giovanni (Mafia boss), Lysandre(Corrupted Philanthrope), Lusamine(Animal-Testing Cosmetics industry), Guzma(Scam Artist), Ghetsis (Profiting Cult Leader), Archie and Maxie (Colluding Oppositional Party Leaders) are horrible people whose cognition you need to change by eradicating ultra beasts who possess them.

Paper Mario
Paper Mario finds a mysteriously pokemon game in the mail (marked as a present from Peach). Bowser designs the game to trap Mario in order to have sweet Peach to himself. He makes the game "impossible" to beat (or so he thinks). The goal is to complete the game in order to escape and save Peach. Pokemon are partners/enemies. Mario would wear red's hat. Your first partner is Pikachu for obvious sales reasons.

Main Characters: Lilligant-Peach, Tyrantrum-Bowser, Shiinotic-Toad, Cacturne-Luigi, Charmander-Yoshi, Misdreavus-Vivian, Mimikyu-Dooplis

Fire Emblem
Pokemon battling alongside Fire Emblem characters...pretty self-explanatory.