So the biggest problem here is to re-breed everything we've done in the past to get the new Eggmoves/abilitys.
What about, on the final of the dungeon, put an npc to teach you eggmoves/abilitys to the oldest pokemons (with a certain cost).
This is a simple way to solve both of the problems of rebreeding everything to get the new moves/abilitys, and at the same way, some of the content (the dungeons) will be use usefull for new pokemons.
Im trying to express myself, sorry for my bad english.