Hell yes.
I could go into a long and detailed rant about why I don’t like the HM system, but since you agree with me anyway, I’ll spare you.
You’re quite right that the simplest answer would be to make the various field abilities into inherent characteristics of the Pokémon requiring no special training, a la Pokémon Ranger. I have floated one other method in the past – I was trying to kill two birds with one stone and also make the Unown useful in the game, so I suggested the introduction of special tablets that could ‘seal’ sequences of Unown and then produce supernatural effects in keeping with the sequence used – so a tablet reading SWIM, for instance, would allow you to cross water. Basically, you gain these abilities by capturing a large number of different Unown, something the games have always encouraged you to do but never adequately rewarded.
I could go on, but I have an entry on this subject planned for the… well, I don’t want to say ‘near’ future because that’s tempting fate, but… yes.
