Maybe a dark family member who has been banished from the family long ago. Now that Harry and his sister are becoming more powerful, this family member resurfaces to claim what they think is rightfully theirs. They could use dark magic to try and get rid of the siblings.
It could be a jealous wizard who feels that Harry and his sister are getting too much attention in the wizarding world. This wizard might try to undermine their achievements and even put them in danger.
It could be a new, self - made villain. Maybe a rogue ninja who was once rejected by the Hidden Leaf Village. He blames Naruto for his misfortunes and decides to target his sister as revenge. This villain would have his own set of unique and dangerous jutsu, which Naruto would have to figure out how to counter in order to save his sister.
It could be a dark wizard who is jealous of the Potter family's fame and power. He sees Lemon as an easy target to get to Harry and plans to use her to lure Harry into a trap.
A powerful and greedy Pokémon collector could be the main antagonist. He might try to steal Ash's Pikachu or other strong Pokémon from them. He would constantly be one step ahead, setting up traps and obstacles for Ash and his sister during their travels.
It could be a member of Naruto's family who is fueling the neglect. Maybe an older relative who believes that the sister has more potential or is more worthy of attention and resources. This person could actively try to keep Naruto down.
It could be Frieza. Since Frieza has a history of hating the Saiyans, he might see Goku's sister as a new threat and try to eliminate her.
It could be an archaeologist who has been corrupted by the power of an ancient artifact related to the mummy. This archaeologist wants to use the mummy's power for his own gain, like becoming immortal or ruling the world. He would be constantly trying to stop Harry from helping the mummy.
It could be a powerful dark wizard who has also gained some supervillain - like powers. This antagonist might be jealous of Harry's newfound superhero status and wants to destroy him.
It could be a rogue Death Eater who survived Voldemort's fall and blames Harry and his sister for the downfall of their cause. This Death Eater might be more cunning and powerful than the others, and he targets Harry's sister specifically because she represents a new threat to their dark plans. He might try to use her as a pawn to draw Harry out and then destroy them both.
It could be a dark wizard who wants to use Harry's sister for some dark magic purpose. Maybe he believes that her blood or her unique magical essence can be used to open a portal to a world of dark magic or to resurrect an even more powerful dark force. This antagonist would stop at nothing to get his hands on her.
In some cases, it could be that the magic system itself is the antagonist. For example, if there are ancient magical laws or curses that are affecting Harry's judgment and making him act against the Weasleys. The fanfic could then be about how they all fight against the constraints of this magic system to reconcile.