Well, perhaps in the other universe, Harry finds that Voldemort is actually a hero. This would completely flip his understanding of good and evil. He could also meet alternate versions of his friends. For example, Ron could be a super - intelligent wizard instead of the more laid - back character he is in the original universe. And Hermione might be a powerful athlete rather than a bookworm. This would create a lot of interesting interactions and character development for Harry.
One idea could be that Naruto arrives in a world full of magic. He tries to understand and master the new magic system using his ninja skills as a base. For example, he might find that his chakra control can be adapted to control magical energy in a unique way.
Another possibility is a new character that is unique to the other universe. This character could be jealous of Harry's arrival and the power he might bring from his own universe. So, this character tries to stop Harry from exploring and potentially changing the new universe.
One idea could be that in this alternate universe, Hufflepuff is the dominant house in Hogwarts. They have a secret society within the house that holds the key to an ancient magic that can save the wizarding world from a new, unknown threat. And the main character, a Hufflepuff student, discovers this by accident and has to take on the responsibility to gather the members of the society.
One idea could be exploring the origin story of the 'Master of the Universe'. Maybe he was an ordinary person who stumbled upon a powerful artifact that granted him his powers. Another could be a story where the Master of the Universe has to face a new, unexpected enemy that challenges his powers in ways he's never experienced before. For example, an enemy that can nullify his powers temporarily. A third idea is a 'what if' scenario, like what if the Master of the Universe lost his memory and had to rediscover his powers and purpose while being hunted by his former enemies.
Another plot could be that Harry is mistaken for someone else at Ouran. He then has to navigate through the misunderstandings while also trying to figure out how the Ouran world, with its own set of rules about class, social status, and relationships, compares to his world at Hogwarts. There could be a lot of comical moments as he tries to fit in without revealing his true identity as a wizard.
One idea could be Harry making new friends in Salem who have different magical abilities than those he knew in Hogwarts. Another could be him encountering a unique magical creature native to Salem. Maybe he gets involved in a mystery related to an old Salem witch trial that has some lingering magic.
One idea could be Harry making new friends who have no idea about his wizarding past and he has to keep it a secret. Another could be him joining a unique university club related to magic in a very subtle way, like a club for illusionists where he can use some of his real magic skills without being detected.
Another idea is a fanfiction that focuses on the Marauders' time at Hogwarts. We could see more of their pranks, their relationships, and how they dealt with the growing threat of Voldemort. For example, exploring how Sirius and Remus' friendship developed during those years in greater detail. It would also be cool to see more of James Potter's character before he became Harry's father.
One idea could be an alternate universe where the ponies have different elemental powers. For example, instead of Twilight Sparkle being a unicorn with magic related to friendship, she could control time. This would change the entire dynamic of the stories and the relationships between the ponies.
One idea could be exploring how the characters' relationships change. For example, if Deku was a girl, how would her dynamic with Bakugo be different? Maybe Bakugo would be more protective in a different way. Another plot could focus on how the female versions of the male heroes deal with the challenges in the hero society, like discrimination that might be specific to female heroes. Also, a plot could revolve around a genderbend All Might and how she inspires the new generation of heroes.