How to fix pokemon

Or make it so Poke's that SHOULD know the HM(IE winged/flying types with Fly, fish/aquatic types with water HMs like sure/waterfall) have it as a natural ability. If the Poke was caught wild, it'd have the ability already, if you bred it(or evolved it from a Poke that can't do it, like Charmeleon > Charizard learning how to fly) it'd learn how to do it eventually(no bird can know how to fly right after hatching and such), like at 20 or something.
But yeah, limit it to 2 abilities per Poke.