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Holy shit it’s easy. Just make gym leaders and the elite 4 plus any boss type battles (like giovani at Sylph Co.) ocassionally switch out Pokémon, have at least one Pokémon on their team to provide coverage, and give them decent move pools. It’s not that hard to implement some of the AI needed for that.
Also stop giving gimmick ways to rechhallenge gym leaders. Just let people rechallenge then whenever they want. Every third time you beat them they’re Pokémon’s levels increase by like 5, they swap out one of their Pokémon or a receive a few different moves.
Whoa! Pokémon’s now fixed.