well have any of you played Arcanum by troika studios. that was a skill system i liked.

Basically when you leveled up you were given one skill point and you could spend said skill point on any skill in one of many classes which included magery, social skills and and technological item crafting. but here is my point (and this kinda fits in with some of the posts above mine) is that you could gain exp and advance your skills on your own but if you went to a trainer you would get your skills enhanced in certain ways.  lets say your char was an archer and he trained himself instead of going to a teacher in the game he would still be a high lvl archer if the person playing put his or her mind to it but said archer would still be weaker then a person who decided after training their archer for a little bit to send them to a trainer who would then train them maybe giving them a bonus to speed and accuracy,or lets say alchemy that would be a bonus to rate of success or something

boy this is getting long ... but in any case all im saying is that  maybe you could make the trainers essential not by making them the only way to upgrade your skills but by making you more effective more powerful if you will. And  somewhere to store your loot would be nice as well