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I've been in love with a distant fantasy prequel to Pokemon, before modern technology and before even pokeballs. You have this medieval fantasy with gigantic beasts wandering the lands, and humans utterly dwarfed by them. Instead of Humans being in control and using Pokemon to make their world function, this world belongs to the Pokemon, and humans have been at their mercy.
I've had a thought similar to how Lightsabers come from crystals, maybe the early predecessor to pokeballs were soulgem type elemental stones, used to trap or contain a mons essence. So gradually you, the player, would begin to conquer smaller lower level pokemon and use them to traverse and become the dominant figure in this vast, hostile land.
pic related