I recommend you taking a long look at Magicka.

These guys did wonders on this game. It's all about using different combinations of magic. For starters you can throw a rock at enemies, then you can set it on fire, or freeze it, or add some lightning to it. It was all about trial and error to find the best spell(s) for the situation. I thoroughly enjoyed it.

another game that used the school theme well was Bully. Classes upgraded you skill in different areas. english made you able to get stuff from people easier through talking. gym made you stronger and faster. shop allowed for creating better items.

Did you see the movie The Last Airbender (2010) or the series? In this case there are 4 nations Earth/Fire/Water/Air and in order for the Avatar to learn each ability he needs to travel to each nation and learn it from the corresponding master/s.

The same way dragonborn was unique among others in TES Skyrim, the same happen with the Avatar, there is no other like him, at least at that time in history, I think this is something that makes the player be more interested, more fascinated, just an idea to have in mind when creating a story.

I think there is something missing in role/magic games like TES/The Witcher/Age of Dragons, in this games the player needs to work hard to gain new skills but applying/using them is as simple as pressing a button, so what do you think (leaving for a moment the magic skill learning process behind) about the player making series of things (different key combinations for example) to unleash a given Spell, like the key combos in Indygo Prophecy/Farenheit, or else: the typical moving bar metter usually found in tennis games or golf games, if you fail to click your mouse when the bar gets to a certain point then the spell will fail, like this you could control spell power also if you want. It could be real time fighting or turn based attacks, something like in Pokemon. All these are very nice topics for brainstorming, fascinating stuff.

I think it would also be interesting, though kind of platform-dependent, on having some physical interaction with the game in order to properly cast spells. For example, you'd have to memorize actual movements with your hand or a wand for something like a kinect, plus an incantation. I mean, I guess you could also have some sort of complicated mouse movement for a vanilla PC game, but that's not nearly as fun-sounding.

You could also have stats under the guise of "grades," so instead of leveling up and getting +4 Fire Magic, you would take a Fire Test and get an A- and be "qualified" at "Fire Adeptness: Junior Level" on your "academic magical transcript", and move onto the next more advanced class somewhat like real life school. Think of OWLs or NEWTS in Harry Potter.