This is an interesting question. One can learn so much from reading alone but, as they say, experience is the best teacher.
It would be great if a system could be setup in such a way so that the player to learns the basic skill from a book, and with a few levels after, get an upgraded version of that skill. That kind of system might be horribly complicated with any RM engine I'm aware of, though.
If it's any consolation, when I attempted a non-standard skill learning system for Matsumori Days, I ended up using a class switch to "fix" the skill listings of my characters.