Something that I think would be awesome is having a partner (something anthropomorphic, like a spirit or an actual person) that you can acquire at each level or can level up with you. Partners could have a single power that students could activate once per class or per day. Powers could increase in usefulness by level of either the character or the partner (if it has a separate leveling mechanism). Powers may include granting a small amount of XP or GP, refilling some HP or AP, or any sort of thing really (especially if customizable by the teacher).
If an adaptation were added to the pet system, it could build easily off the current system and maybe add an evolution aspect to the pets as part of training / leveling (a la Pokemon and similar games).