You could try and remove the humans as antagonists completely. Re-imagine RSE without Team Aqua/Magma. The Delta Episode happens first, the meteorites cause all kinds of problems that the protagonist has to solve (Mega Evolving Wild Pokémon, Pokémon Attacking Villages, Ect) and the climax is...
In the traditional games, you need an antagonist. I suppose it could be a Pokémon (like Necrozma/Mewtwo), instead of a team, but you need something to break up the monotony of "hey I beat a gym, let's go beat another gym."
It would be a major shift from the traditional games, but I think it...
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