a few thoughts I had for rules variations that could have huge impact on the world being played in:
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non-hermetic vis: why should all the vis fit nicely into hermetic theory? Perhaps there is some "Nu" vis for the amazons, or Viglio vis that the order doesn't understand, or detect...
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magical entities as a study source- if a magical entity is willing to teach their art, perhaps allow a SQ equal to 1/5 their might plus com (+3?) with a level limit equal to their might?
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teaching assistants- as with a craft ability, a teaching assistant can add 1/2 their teaching score to that of the primary teacher, provided the level of the student in the topic subject is lower than that of the TA. Even when it is not a TA allows more students to be taught as per adding 1/2 their teaching ability...