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I actually like story and shit so I'll bite
>pokemon league is more present as an actual organization in the story; you interact with its representatives (gym leaders and others) in more ways than just battling them; they're also a quasi governmental organization for the region
>as a promising trainer, they want you to represent and promote the league also
>the league is actually fifa tier corrupt
>team whatever's primary objective is to subvert the official league with guerilla journalism/humiliating its trainers with public defeats
>leader of team whatever is a charismatic narcissist whose professed goals are anticorruption but is mostly leaving anarchy in his wake by tearing away at the institution central to the region
>ultimately as a prospective champion you have to choose whether to support team whatever or pokefifa, or stay out of it entirely and just go clear gyms and shit
the thing is though op it doesn't really matter what your plot outline is. what's important is the execution. with marginally better execution:
>black/white could've been an introspective and meta look at the core concepts behind pokemon
>dppt could've been a critique of the insular utopianism that comes from forming an ideology without ever talking to another human being (cyrus is a fucking weird cunt)
>rse could've been about the perils of naive activism
and so on
you can tell a good story with almost any framework