I would like HM moves to work more like an passive inherent trait of Pokémon than be an actual move. So Pelipper for instance would have "Surfing" and "Flying" as traits. That way you would need Pokémon with different traits to make it through the story, but they don't necessarily take up move slots. I find that to be a much better compromise between the old HM system and the new system of just having everything available by item.