I like the idea of leveling up the skills you use most, a la Oblivion, but in practice that system is a pain. Perhaps if they tweaked it a little bit, maybe using the pen & paper Call of Cthulhu as an inspiration...
(EDIT: For those out there who don't know the CoC system, every time you succesfully use a skill, you get a "check" for that particular skill. When the play session is over, you test all your checked skills, by throwing "percentage dice" and comparing the result with the level of the skill (which can go from 0 to 99 percent). If the dice result was higher than your skill, it gets better. That way, it's progressively harder to upgrade your skills the higher they are, just like in real life. Of course, we would have to come up with a substitute for the "play session" end, maybe the player could test their checked skills once per day, or maybe there could be a traditional XP system to determine when they would be allowed to test their skills.)
So i'll have to go with the Gothic series approach: every time you level up (through traditional XP you get from most everything, like killing enemies, completing quests and such), you get 10 "learning points" and nothing else. Not one of your attributes or skills go up right away, you have to find trainers and pay them with money AND spend Learning Points to learn a skill or raise an attribute. It's more realistic without being boring, which I think is one of the best aspects of the Gothic series as a whole (especially the first two games, G3 wasn't THAT good).