I'm going to go out on a limb and say that the only way this would be remotely feasible, is by making all Pokemon in X and Y catchable, breedable, and all former event ppokemon catchable and breedable in that one cartridge.
Event Pokemon should be special. Special Ball, Shiny, Special Pokerus that is permanent. Maybe even a special move. They should not be so special that they are uncatchable.
One Trainer to rule them all, One Trainer to find them, One Trainer to catch them all and in the Pokeball bind them. Legend of Legacy.