Bring Back National Dex - Another shameless meme.

See, that's how Generations 4 through 7 worked (and technically Gen 3 as well; since while you couldnt transfer from the Gen 1-2 games, all the Pokemon in the dex could be caught in one of the 5 Gen 3 games and transferred among them). A Pokemon might not be available in the game to be caught, but you could always transfer one in from an old game or trade for it from someone who did.