>>45587008For me, I'd have two "regions", one a smaller island nation that acts as the main hub for towns and such, and the other a larger, undiscovered/uninhabited landmass that serves as everything else.
You're the child of wealthy and renowned archaeologist parents that were sent out to help explore/document this new region, but after a while they and most of the rest of the team go missing. The region's so hostile and dangerous that rescue efforts are slow and apprehensive, so you take your close family pet (the starter you pick while selecting your character) and go to look for them yourself. As you go you help liberate base camps and find out that part of the expedition team went rogue and betrayed the rest for profit, and they're using your parents to help them find rare pokemon. Totem-style wild pokemon and stronger than usual rogue members serve as boss fights, while gyms and the league are absent, a postgame battle tourney in the hub region replaces it.