How would you feel about this? Instead of needing HMs to get past certain obstacles, Pokémon now have skills that they can use in the overworld based on whether or not it makes sense for them to have it(Lapras can ferry you across water, Machamp can use boulders etc.) It's very similar to Pokéride except you have to catch the Pokémon. In addition you can use Pokémon from your portable PC to perform these tasks so you don't have to switch out from your main party. When you register a Pokémon in the dex you can see what skills that Pokémon. This would encourage players to catch more Pokémon and eliminates the burden of forcing bad moves on your main party.