I'm fine with the gamified elements to the extent that they are used in Super Nintendo World, but it shouldn't go any further than that. Asking people to transmit their Pokémon from within the games themselves is an unreasonable barrier to entry that most people will not be willing to go through the trouble to do. Not to mentioned, there would need to be complex technical work to make that possible, and it would need to be indefinitely updated as new games and Pokémon are released.
I'm sure there will be some app integration with catching Pokémon and filling out a Pokédex, but it will be a smaller curated selection of Pokémon that makes sense to be used within the land.