This would make designing monsters, especially bosses, a nightmare. Clearly there would need to be skills that can't even be copied (instant-killing the boss with his own party-wipe skill?! really?!), and at that point, you "lose" skills by having nothing to copy on some fights, despite being barraged with it.

I don't see why blue mages couldn't have a mixture of learning methods myself. Learn general actions with levels, learn blue magic from special quests that involve fighting unique monsters or directly from trash ones like in other games. The coding of the game doesn't stop that. It's not one of those things that would require a rework of the system, but an addition to it. Instead of setting the trigger to "reach level X" or "complete quest Y", you set the trigger to "be hit by X" or "kill Y of Z mobs".