Consider also that many skills are not necessarily intended for PC use. Profession and Craft are the more obvious ones. They are intended to help define the merchants, artisans, etc that the PCs may encounter in their travels.
I've actually long been of the opinion that all modes of movement (including Fly) should be skills - limited in use to those with a means of actually accomplishing them (wings or other means of gliding or flight for Fly, fins / streamlined body for Swim, digits / hooks / etc for Climb, some means of shoving loose mass out of the way for burrow, etc). However, it would require a bit of reworking of the skills system, I think.