Another option is that there could be a secret organization within Naruto's own village that doesn't want him to get stronger under Pakura. They might be jealous of Naruto's popularity or have some ulterior motives. They could try to sabotage his training by spreading false rumors about Pakura or creating obstacles during their training sessions.
It could be some rogue shinobi who are after Pakura's knowledge. Since she's training Naruto, they might see it as an opportunity to get to both of them and steal their techniques. Maybe they were once her enemies or just power - hungry individuals.
The fanfic could be about Naruto's journey of self - discovery under Pakura's training. Pakura might see the potential in Naruto not just as a powerful shinobi, but also as a person who can bring change. She could train him in both physical and mental aspects. Physically, teaching him new combat moves and defensives. Mentally, guiding him to be more patient and strategic. This training could be a turning point for Naruto in his battles against stronger enemies.
There could be new antagonists created specifically for this fanfic. Maybe some dark forces that were sealed away by Asura long ago are awakened. They would oppose Naruto because they see him as a threat to their resurrection or their evil plans.
The Akatsuki could still be the main antagonists. Even with Naruto's training by the Kyuubi, they would be after the tailed beasts. Their goals of collecting all the tailed beasts would put them in direct conflict with Naruto. And they have some really powerful members like Pain and Itachi.
It could be the other Hidden Villages. Since Naruto is becoming so powerful under Danzo's training, they might see him as a threat and try to stop him. Maybe they would send their best ninjas to take him down.
The Otsutsuki clan members other than Kaguya could be antagonists. Since Kaguya is training Naruto, they might see Naruto as a threat to their plans.
The Akatsuki could still be the main antagonists. Even with Naruto getting trained by Mangetsu, the Akatsuki's goals of collecting the tailed beasts would still pose a major threat to Naruto and the ninja world.
The Akatsuki could still be the main antagonists. Even though Sasori is training Naruto, the rest of the Akatsuki might view Naruto as a threat and try to eliminate him. Also, Orochimaru could be an antagonist. He might be interested in the new skills Naruto is learning from Sasori and try to steal them for his own experiments.
Well, in this fanfiction, the Akatsuki could be the main antagonists. They would view Naruto's godlike powers as a major threat to their goals. Since Naruto has been trained by Shendu, his abilities would be unpredictable and extremely powerful. They might band together to try and take Naruto down. Additionally, there could be some ancient demons or spirits that are awakened by Naruto's new powers and they see him as an intruder in their realm, so they become antagonists as well. They would use their own dark magic and powers to oppose Naruto.
In addition to Naruto and Pakura, Hinata could be involved. She has a crush on Naruto, and with him being adopted by Pakura, she might be shy yet eager to interact with him in this new context. Rock Lee could also be in the story. He is always looking for strong opponents and new training methods. Naruto's new situation under Pakura's care might intrigue him, and he could try to learn from Naruto's new experiences. And of course, Orochimaru might be interested in Naruto's adoption as well, seeing it as a way to potentially get closer to Naruto for his own devious plans.
The Akatsuki could still be the main antagonists. Since Naruto is being trained by Shisui, they would see Naruto as an even greater threat. His new skills under Shisui's training could put their plans at risk. For example, if Naruto becomes better at stealth and infiltration, he could disrupt their operations more effectively.