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I will never understand why BR didn't give us something as simple as a story mode, it didn't need much work, a couple of locations, development through dialogue, some cinematics, with different routes to acquire different pokemon along the way and these will be stored in the memory of the game, as well as different endings depending on the character you chose and route, it could be a couple of png images and a text box, leaving a cinematic for the hidden ending of the game.
This way you would have an alternative to have all the Pokémon without needing a copy of DPP, of course it would be more difficult, but that would give the game replayability.
If they didn't want to return to the Shadow Pokemon system, it was enough that every time you defeated a trainer he offered to give you a Pokemon or acquire them through rewards for completing a challenge, or bring back arcade mini-games to win them like in Kanto and this way creating your ideal team.