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Okay hear me out, alien invaders.
You could do it for a 35th anniversary release or something. Aliens invaded the planet a few years back to capture more Pokemon as they had left almost every Pokemon on their own planet extinct. It was a threat so great that every Pokemon protagonist, rival, gym leader, E4 member, and anyone else important from Gens I-VIII united to stop the invasion. You could probably have a cool cutscene to open up the game with this very war taking place where everyone is firing hyper beams at their ships and stuff.
Your adventure takes place during the second invasion. You're a rookie trainer joining the Earth Defense Forces and you pick your starter and go through gym challenges as training to fight said invasion.
There are three ways you could do the fights with the ayys.
1). They just use Pokemon we've always known to be extra-terrestrial, stuff like elygem, clefairy, staryu, solrock and lunatone, ultra-beasts, etc.
2). They use all new Pokemon that you cannot catch during the main game as they all come from the invaders' planet. Postgame will let you catch them because they end up leaving some behind after their retreat. Might even get special balls for it like beast balls.
3). They don't even use Pokemon at all, they just fight you with laser guns and beam swords. You'll have to figure out what their type advantages and disadvantages are and it won't be immediately obvious.