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.
Madara Uchiha (even if it's an alternate timeline situation in the fanfic). He might view Naruto's sister as a key to disrupting the balance of power in the ninja world. He'd use his Sharingan and his powerful combat abilities to try and take her. Naruto would then have to rise to the challenge and find a way to defeat Madara, which would be no easy feat.
Maybe Kabuto. He's a sly character who often works for the more powerful villains. He could be sent to capture Naruto's younger self for some experiment or to gain information. Naruto would need to fight against Kabuto's medical ninjutsu and his sneaky tactics to save his younger self.
It could be a rival archer who has a vendetta against the main archer and decides to target his family to get back at him.
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 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 a rogue ninja from the Hidden Leaf's past who has come back for revenge. Maybe someone who was wronged by the village long ago and has now amassed great power to destroy it. Another possibility is a new enemy from outside the village, like a powerful warlord from a far - off land who wants to conquer the Hidden Leaf for its resources.
Perhaps the story could start with Naruto finding out that his sister is in a secret location held captive by a dark organization. He embarks on a journey full of challenges. Along the way, he has to overcome various traps and face off against strong opponents. His shadow clones could play a crucial role in distracting the enemies while he reaches his sister. Once he does, he uses his chakra to break any bindings and brings her to safety, all while showing his growth as a ninja and a brother.
Perhaps it's a group of mercenary ninjas. They've been hired by someone who has a grudge against Zabuza. They see Zabuza as an easy target when he's alone or vulnerable, but Naruto shows up to spoil their plan.
Perhaps a new and original antagonist could be created for this fanfiction. This antagonist could be a rogue ninja who has mastered a forbidden jutsu that allows him to manipulate time as well. He could be the one who sets up the events that lead to Minato's endangerment, and Naruto has to figure out his motives and stop him while also saving Minato.
It could be a rogue ninja who is using the poochyena for some sort of evil experiment. Naruto has to stop this ninja from harming the poochyena.
It could be a rogue ninja from Tobirama's time who has a vendetta against the Senju clan. This ninja might have been waiting for the perfect moment to strike at Tobirama when he is alone or vulnerable. Naruto then has to face this powerful and vengeful enemy to save Tobirama.