How interesting this magic becomes is totally up to you. You are the writer. You have the magic words. You make the system cool. I can give you some pointers on being unique. Here are some things I have not seen.
- Something other than genetic magic. All magic to date has been an inborn trait. The characters have the right genes or are the right species, and, suddenly, they can do teh magickz. Make magic a skill anyone and their grandma could potentially pick up. If you want to make it rare, make the locations for formal instruction in magic rare or hard to get into, or make all the instruction manuals jealously guarded artifacts.
- Magic with a life of its own. Nowadays, magicians seem to call magic forth from the wells in their mind or some such BS. What if magic was like a sentient species of its own, that had its own emotions and - at least partially - dictated what it was going to be used for and when? What if it was another group that magicians had to hammer out a Terms and Conditions with? What if magic was a total asshole that didn’t want nothing to do with no one? What if magic had its own opinions, its own agenda, and and its own plots? The possibilities are endless.
- Magic philosophers. Big, complex, unsolvable puzzles have always attracted
nerdsbrilliant geniuses trying to make sense of it all. Have a magic system with its own rules that are followed consistently and not broken by the hero for the sake of drama. Have people trying to make Newton’s laws or Einstein’s principles or Mendel’s theories work with whatever form of magic you have. Explore the relationships. It seems that everything else (gravity, atmosphere, genetic makeup) in a fantasy world is similar to Earth, so why not give its laws a shot? If every reaction has an equal and opposite reaction, what happens when a magician fires off a fireball? Where is the opposite reaction? Does it burn her mind? Take the form of a shock wave? Kill the nearest goat? This would work best if you were a math geek.
- Different types of magic in the same universe. The only example I can think of is the Inheritance Cycle, by Christopher Paolini. It has the typical magic system (source and rules are unexplained and broken for drama, respectively), sorcery (enslaving souls), and possibly holy (an illusion of a dwarf god). Only the Magic System was really explored, but it would be great to develop several kinds of magic and let them and their users interact with one another. Does magic X cancel out magic Y? Can magic T only be used by a certain group, but can on occasion be wielded by group H?
- Limited magic. I’m not talking only naive teenage boys with swords. I’m talking magic limited by age, time, emotion, and other factors. Maybe magic power grows or decreases as one ages. If children are born with crazy amounts of magic, those parents are going to be walking on eggshells hoping their kid doesn’t turn them to worms during the Terrible Twos. It would definitely change the structure of the society and how the youth is seen and treated. As for time, I’m referring to the occurrence of specific events that would trigger the magic. Maybe only new mothers or someone who’s lost a friend can use it. Maybe women can only use it on their periods. Maybe it only happens on birthdays or for one year of your life. Maybe, maybe, maybe … I’m sure you can come up with some better alternatives.
- Practical magic. We never see magic building a dam or growing crops or making clothes or cleaning waste pits. It would be nice to have a magic system that does something other than blow stuff up.
- Chinese elemental magic. Use water, wood, fire, metal, and water instead of the traditional fire, water, air, and earth. Plus, the Chinese elements have a crapton of rules, martial arts, ceremonies, and symbolism already attached to them that you can play with. As always, do lots of research, as this is a IRL system.
There are more super cool options explained here.