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I would make it so:
>Beginning of the game is straightforward like rby
>10 badges
>Gap between gyms is longer (like from Santalune to Cyllage)
>Each gym leader would have a story event attached to them to flesh out their characters
>Villians aren't some over the top genocidal group, but more grounded like Giovanni
>After about 2-3 gyms a large story event would take place
>Climax of main story is right before the 8th or 9th gym so a new story arc concerned with the Pokémon league can get into gear
>Elite 4 is standard fare, 5 Pokemon, Champ has 6 and also uses some sort of strategy (trick room, rain etc.)
>After Elite 4, another major story event unfolds concerning the box legend (this is where your over the top shenanigans occur)
>Possible other story elements in postgame like searching for and battling some of the protagonists from past games or hunting down a criminal with Looker
