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Assuming we’re starting from a full wild area game, here’s what I came up with.
>Level scaling:
Each biome has a wide level bracket that Pokémon there spawn in based on the average level of your team and # of party members. Additionally, gym leader Pokémon will never be a lower level then you.
>Botw style nonlinearity
Once you get your starter and are out of your home town, that’s when the linearity stops. Each gym is still higher level than the last, but you totally could go fight the 8th dude and his lv60 dragonite with your lv.5 squirtle if you want too and are welcome to try.
>terrain navigation
You’d be able to use the Pokémon you’ve caught to help you navigate the open world. Climbing mountiansides, cutting through forests, swimming through the ocean, etc. figuring out what you can do is reliant on experimentation. This breaks the linearity further by allowing the player to create their own adventure as they work towards their goal.