Hm, why not replace the Breeders with rebattleable trainers that are focused on certain Pokemon types, similar to the trainers in the Grand Hall in Reborn?
Right now, with the lack of level cap and free XP Audinos , people can very easily overtrain early game and just sweep everything with one Pokemon.
If you really don't want to introduce a level cap for X amount of badges, maybe at least make the player earn that XP?