Some random plot ideas:
Bad guy is a televangelist that has been persuading trainers that stronger trainers should be allowed to their capture their opponent's Pokemon directly. More of these trainers are encountered throughout the game (and i you lose to them, a random Pokemon is stolen, to...
Here's an idea: no villainous team at all. It's a crutch and it's never made for a good story. Even in BW, with the best story in the games, the best part was N and Ghetsis, not Plasma.
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