I hate to tell you this, but you brought it on yourself. I can't find the reference now, but another forum I'm on discovered that using AR to level up has the opposite effect - your Pokémon need a LOT more experience to level up that way! It's one of the levels of AP, sort of, but no one bothered to figure out a way around it since all you have to do is play through it legit.
Long story short, you messed up your game. You want to get through it, you need to restart. Otherwise you're going to be spending a LONG time grinding.