If you really want to create something new, fresh, and not clichéd, maybe don’t write a magic school novel? Those have been done to death by now, just like vampire werewolf love stories.
However, you have made up your mind, I would suggest don’t worry too much about appearing original. No matter what you do, your novel will be compared to Harry Potter. But in case it is any consolation, that will happen no matter what you write. JK Rowling herself was accused of plagiarising elements of Harry Potter from multiple sources. She was even accused of stealing from Neil Gaiman, a charge that Gaiman himself dismissed on his blog:
Back in November I was tracked down by a Scotsman journalist who had noticed the similarities between my Tim Hunter character and Harry Potter, and wanted a story. And I think I rather disappointed him by explaining that, no, I certainly *didn’t* believe that Rowling had ripped off Books of Magic, that I doubted she’d read it and that it wouldn’t matter if she had: I wasn’t the first writer to create a young magician with potential, nor was Rowling the first to send one to school. It’s not the ideas, it’s what you do with them that matters.
Anyone who knows anything about how stories are written will tell you that books feed on older books. Ideas get remixed into new ideas and the very genre of fantasy survives on a foundation of accepted signs and symbols.
Having said that, there are always new things you can do to make your tale unique.
You can make your story about things other such stories are not.
- Maybe your hero is not an orphan and has healthy parents who would rather he focused on science. Can make for a nice science vs magic dichotomy.
- Maybe your school as a quota system for under-represented classes and that’s how he got in and has to now prove himself and gain the respect of his classmates.
- Maybe he discovers he not very good at magic and has to now worry about his career prospects after passing out.
- Maybe his school has incompetent teachers and he has to take extra tuition classes on the side.
You get my drift. In my experience, what makes fantasy enjoyable is not the wild flights of imagination. It is the places where it connects with the real world. Go wild, but try also to go domestic.