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Honestly, just trim it down to the basics and see what we have.
Make it more of an adventure with you and your Pokemon rather than one with you always feeling like the side character amidst all the other poorly-written shitters. Of course, you can always have rivals and stuff, but at least make them actually neat characters instead of the overdone 'friendly rival that bends over constantly' or 'sensitive female loli for those sick lolibux'. Ex-evil team, thugs, rich snobby dorks; you have a lot of untapped choices.
As for the story itself, strip that a bit too. Not even fucking Pokemon game needs to have some megalomaniac villain who wants to destroy the world for some reason. I fucking hate this running shit. You can have villains, but make them less one-note. Go back to the basics, think Team Rocket. Mafias are always cool.
Pokemon doesn't have to have ridiculous stories, just go back to the basics and go from there.
