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Pokemon storylines usually boil down to two main plots:
a) Take down the evil villain/team who wish to mess with the state of the world OR
b) Get involved in family drama that has escalated to the point where the world is threatened.
So let's come up with alternatives:
1) The player starts off being the son/daughter of the Champion. The story revolves around the former Champion losing touch with reality, becoming homeless and desperate since they lost their former glory. The player goes around the region to assist the former Champ have one more battle with the current Champ for some purpose and then the player can choose which Champ they wish to win. Player then faces off against the Champ and wins, roll credits.
2) Pokemon have been disappearing from the region and the Player has to find out why. This could've been done with a Kalos-sized Dex and once the player has found out the cause/defeated the cause, more Pokemon become available.