Perhaps there are some anti - Uchiha elements within the village that are not happy with Naruto adopting Sarada. They could try to undermine her training or create problems for Naruto and Sarada. They might spread false rumors or try to isolate Sarada from the rest of the village.
Well, one possible plot could be Naruto seeing Sarada in a difficult situation, perhaps without proper guidance from Sasuke who is often away. Naruto, having a big heart and remembering his own lonely childhood, decides to take her under his wing. He could teach her some of his signature jutsu and also instill in her the values of hard work and friendship that he learned from Iruka and his friends.
It could be other villages that see the alliance between the Raikage and Naruto as a threat. For example, some of the more power - hungry villages might fear that the combination of the Raikage's strength and Naruto's abilities would tip the balance of power in the ninja world. So, they would try to undermine their relationship or even attack them directly.
Orochimaru could still be an antagonist. He might see Naruto as a threat especially if Kakashi is training him intensively. His goal of obtaining power could lead him to target Naruto.
In the Naruto world, it could be Orochimaru. He might be interested in Naruto's newfound Pokémon - related powers and try to capture him to experiment on him. Orochimaru is always after power, and Naruto's unique abilities could be very appealing to him.
Another possibility is that some rogue ninja who have a vendetta against Hanzo might target Naruto as a way to get back at Hanzo. They could see Naruto as Hanzo's weakness and try to harm or kidnap him, which would then lead to a series of battles and confrontations in the fanfiction.
One possible antagonist could be Frieza. Since he's always been interested in powerful beings, the presence of Kal - El with his superhuman abilities might draw Frieza's attention. Frieza could see Kal - El as a threat to his plans of universal domination and try to eliminate him.
It's possible that some of the more traditional and strict gods could be antagonists. They might view Aphrodite's act of adopting a mortal boy as going against the natural order. These gods could try to separate the boy from Aphrodite, either by tricking the boy or by putting pressure on Aphrodite. There could also be a dark force or a cursed entity in the story that targets the boy because of his connection to Aphrodite, seeing him as a way to get back at the goddess of love.
Danzo might be an antagonist. He's always been power - hungry and might see Naruto as a threat, especially if Kakashi is guiding and protecting him. Danzo could try to undermine Kakashi's efforts to raise Naruto and might even send his root agents to spy on them or cause trouble.
One possible antagonist could be Sabretooth. He might see Wolverine's newfound fatherly relationship with Peter as a weakness and try to use Peter to get to Wolverine. Sabretooth could be jealous of the bond Wolverine is forming and want to destroy it.
The Ministry of Magic itself could be an antagonist. If they don't approve of Hermione's adoption due to her age or some bureaucratic reasons, they could try to take the baby away. They might think she's not fit to raise a child, which would create a lot of conflict in the story.