>>32080541By not treating every region as an entire region, but instead treat all of them as one, grand region. Only the main routes and cities of each region and those important to missions would be available to you during the story (which would be one hell of a long story), and the rest of every region would be post-game areas.
Maybe mix it with some sort of open-world theme, like Zelda: Breath of the Wild. You start in one region, and you're allowed to go anywhere you want in the entire world. Depending on which route you take, the story unfolds in different ways and you're required to do different tasks and missions in order to save the world.
Let's say you start in Kanto and your first thought is to get the hell out of there as quickly as possible and you travel to Hoenn as soon as you reach Vermillion City. In Hoenn, the story unfolds and you have to befriend Rayquaza to suceed. However, if you had gone to Unova instead, you'd have to befriend Zekrom or Reshiram instead.
This would of course require the story to be something that can happen anywhere and everywhere at the same time, so no matter where you are, the story still happens. I imagine something like Arceus dying and the universe slowly crumbling, and you'd have to somehow acquire the Azure Flute to reach Arceus. You could do this by either travelling to Unova and find Meloetta, travel to Johto and then Sinjoh to use the Unown, or to travel to Sinnoh and ask Cynthia and the Lake Guardians for help.
