Perhaps Flitwick discovers Harry has a natural aptitude for a particular type of magic that is not commonly taught. So he takes it upon himself to train Harry privately. This could lead to Harry having a special role in a future conflict, like being able to counter a dark magic spell that no one else can because of this special training.
One idea could be that Harry discovers a time - traveling device and goes back to Tom Riddle's childhood. He decides to take Tom under his wing and raise him with love and kindness. As a result, Tom doesn't become Voldemort and instead uses his magical abilities for good.
Harry might develop a different set of values. Flitwick has his own way of looking at the wizarding world. Under his care, Harry could grow to value knowledge and magical finesse more than he does in the original story. This could lead to a Harry who is more diplomatic and less impulsive when dealing with other wizards and witches.
A possible plot is that Merlin disguises himself as an ordinary wizard at Hogwarts and secretly mentors Harry. He could introduce Harry to magical creatures that have long been forgotten in the modern wizarding world but hold great power. He also might help Harry unlock some latent magical abilities within him that are related to Merlin's own magic, like the ability to communicate with magical spirits that can offer valuable advice in the battle against Voldemort.
One plot idea could be Mal struggling to fit into the Underworld society that Hades rules. Since she's from a different world in Descendants, adapting to the dark and often chaotic nature of the Underworld could be full of challenges and interesting character developments.
In this type of fanfiction, a possible plot is that Poseidon raises Percy away from Camp Half - Blood to protect him from the prophecy. As Percy grows up, he becomes more in tune with his water powers. He could then have adventures in the ocean, like finding lost civilizations or facing off against sea monsters that Poseidon sends his way to test him.
One possible plot could be that Flitwick focuses on teaching Harry advanced charm spells. He might see Harry's potential and take it upon himself to train Harry privately, away from the prying eyes of Snape or other potentially hostile teachers. This could lead to Harry having a new set of skills that come in handy during battles.
In some fanfictions, Dean might raise angels with a special purpose. Like he raises a group of angels to help him save Sam who has been trapped in a different dimension or something equally dire. The angels have their own motives and secrets, and as they work with Dean, all these secrets start to unfold, leading to a complex and engaging story.
Maybe it's about Harry learning some advanced magic spells from Flitwick. Flitwick could be teaching Harry unique charms or how to use his wand more effectively.
Well, in fanfiction, Flitwick could be portrayed as having a deep understanding of ancient protective magic. He might use this knowledge to create a sort of magical perimeter around Harry. He could also enlist the help of other magical creatures or objects within Hogwarts that are known for their protective qualities. For instance, he could get the help of the house - elves, who have their own brand of magic that could be used to keep Harry out of harm's way. And he may constantly be on the lookout for any signs of danger directed at Harry, using his magical senses to detect any malicious intents.
The character of Filius Flitwick himself is fascinating. He's a small but mighty wizard, and fanfiction allows us to explore more of his backstory, like his days as a student at Hogwarts perhaps. His expertise in charms also gives a lot of scope for interesting plotlines, such as him creating new charms or solving charm - related mysteries.