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I was thinking about this earlier today.
I'd like to see a where you play as an assistant to a professor, catching pokemon and gathering information for the pokedex. Players would have to make and grow their own supplies, like growing apricorns to make pokeballs instead of buying them, or growing berries to make potions to heal wounded pokemon. As you fill in the pokedex and help locals you gain access to more locations, where you can find new resources, different color apricorns for catching stronger pokemon, and new pokemon to catch and research. The pokemon you catch could be used similar to how they do in the Pokemon Ranger games, where instead of useing them for battle, you have them to help explore new areas. In the end you need to track down the legendaries, or maybe stop an evil team who's trying to use a legendary for their own purposes.
What about you guys?