We don't need HMs, what we need are Pokemon like... I dunno, talents or some shit, determined by nothing other than their bodies. Let them have as many as it makes sense for their body to have.. Like...
>Big Muscles, Psychic Power - Push boulders, crates, etc around>Nimble Arms, Sticky Legs - Climb up walls and other surfaces>Sharp Claws, Strong Jaw - Get through thick foliage >Heavy Knuckles, Tail Cracker, Power Kick - Smash rocks and ice and stuff>Carrier - Let you ride your Pokemon for faster movement>Air Carrier - Let you fast travel ala Fly>Sea Carrier - Let you move over water by riding Pokemon>Sub Carrier - Let you dive under water freely by holding onto your Pokemon>Long Body - Stretch to let you move over gaps>Air Mover - Clear away fog and like, poison mist or whatever>Flashing Skin, Bright Eyes, Body Fire - Light up dark areas I realized too late that
>>41392440 already said basically the same thing. Late game you could get actual tools to do these things just in case your Pokemon can't, like a Pick or a Flashlight or something.
Like, take Beedrill for example. Give it Air Carrier, Sharp Claws, Sticky legs... Give Magikarp Sea Carrier and Sub Carrier and let you go on adventures with your wimpy little fish friend.
Honestly, it'd only work in an open world setting that actually has shit to do and a proper sense of scale. 