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They need to stop limiting our choice in order of Gym/Trial.
Kanto and Johto both featured moments where we could collect badges in different orders. I think they didn't go far enough. The map and gyms should be dynamic, scaling to our party so we can tackle them in any order I want.
Make an open-world map. Make the routes actual roads where you'll find the most trainers, and a few trainers out in the wilderness off the routes, where there are more Pokemon. The Legend of Zelda managed to go open-world, why can't Pokemon? Is it because there's no precedence in Pokemon? Screw that, there was no precedence for what we got in Alola either.