GF and Square-Enix make a deal to have a pokémon world in a Kingdom Hearts game. Imagine results ITT.
Set in a main-game region (with humans) or in a Mystery Dungeon setting?
Trainer or Pokémon party member?
Villain?
Both serious and joke answers are welcome.

Human party member might be Red, his attacks comsisting of him sending pokémon out to use elemental attacks, working like the party's magic (Pikachu-Thunder, Fire mon, Water mon with Ice move. maybe a fighting/normal for melee)

Pokémon party member: Mewtwo, Lucario, Zoroark or even Mew.

Villain might be a legendary (Mewtwo, Darkrai, Giratina most likely) or some Villain team leader who uses a legendary pokémon in the final fight. (ie Giovanni-Mewtwo, Giovanni-Birds, Archie-Kyogre ecc)

when you complete the world you get a ball with a Pi(ka)chu who acts like a summon for the rest of the game