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Would a Kingdom Hearts-style RPG, ditch the story, make it a Pokemon-based Feudal Era type thing, where warriors/fighters/some espers, have Pokemon companions. Much like the anime they wear some type of clothing or insignia that has them resemble their companion. Using their Pokes as support, they battle other human/Pokemon teams.
Main character (thought about this in my head for a bit) is from a village of shinobi that, at a young age, helps choose a companion from the several animal-like Pokes that determine their styles, such as Growlithe for Fire-style and ferocious attacking or Taillow for swift, fluid fighting.
In my canon, the main character instead chooses one of the temples attendant Pokemon, a Meditite. Working with the Medicham it eventually evolves into, he develops Fighting skills similar to that of his companion, without the Psychic powers.
