I don't understand your problem. If you don't like the ancillaries a character has got then just transfer them to another character who either doesn't have any or is about to die. If you're building academies then you must be far enough along in the game not to be short of a few characters. And if you are then just bribe them from another faction. You'll tend to build academies in your core cities anyway, which is where the majority of your characters will appear.