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I've wanted a Pokemon game where you're a settler in a new region for a while now.
I'd prefer for it to be set in the past, and for you to be apart of a team of trainers, professors, biologists, architects, technicians, etc etc who just came from a seperate region to this landmass to settle the region and explore and document the entire region and its undiscovered Pokemon.
I'd like for the region to be based on Scandinavia, as there's a lot of potential for awesome lore and great looking wilds that have diverse ecosystems and biomes.
The game would be very open, and you'd be able to do pretty much whatever you want to help with the settlement effort. Whether that be battling to clear out Pokemon threats, researching to discover how the Pokemon native to this region behave, catching and collecting undiscovered species of Pokemon for research into their species, helping to build up the towns by collecting resources and surveying land, all that jazz.
The main antagonists would the legendary duo of the region that don't want humans settling in their home. You'd have multiple encounters throughout the game where they do shit like destroy research, ravage towns, attack people. Stuff that an animal would do when defending its territory.
Your main goal would to be to show them that you mean no harm, and that people and Pokemon can live in harmony in the region.
And for the Gyms I think it'd be pretty cool that if during the game you also helped estabish and build up the League along the way, you could choose which towns and what type the Gyms would be, and then when they're built you can take them on.
Then after all the Gyms are built, the Pokemon league is as well, and there's a tournament to decide the Elite 4 and Champion. If you win it, you become Champion. Or if you place Top 5 you become one of the Elite 4, and can them try to claim the champion title. But if you lose you have to do the league normally.