>>34094434I think a large "team" of wild or abandoned Pokémon that found a way to keep themselves from being affected by Pokéballs and wanting vengeance against humanity. It would put a highlight into the Pokémon themselves and how they think in their own ways as opposed to trainers who seem to only have Pokémon as extensions of themselves.
It'd also make it clear that Pokémon have the capacity to act evil, rebellious, and generally malevolent without a trainer influencing them.