The Akatsuki could still be the main antagonists. Even with Naruto being trained by Minato and becoming godlike, the Akatsuki's goals of collecting the tailed beasts would put them in direct conflict with Naruto. Their powerful members, like Pain or Itachi, would pose a great challenge to Naruto, despite his new skills.
It could be that an old enemy of Minato returns. This enemy might have been in hiding for years, biding their time. Now that Minato is training Naruto, they see it as an opportunity to get revenge on Minato through Naruto. They might have some special abilities that can counter Naruto's godlike powers, at least in the beginning, creating a tense and exciting conflict.
Maybe a new group of powerful ninjas emerges as the antagonists. They could be jealous of Naruto's rapid growth under Minato's training. This group might have some dark and forbidden jutsus that they use to try and take down Naruto. They could be former students of some evil ninja master who wants to rule the ninja world and sees Naruto as a major obstacle.
The main antagonists could also be a group of rogue ninjas who have made a pact with some meta - humans from the Flash's world. They could be after Naruto because they want to use his connection to Barry Allen to gain access to the Speed Force. These antagonists would be a combination of the stealth and trickery of ninjas and the super - powers of meta - humans. They could create a lot of chaos in both the Naruto and Flash worlds, forcing Naruto to use all of his newly acquired skills and powers to stop them.
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.
One potential antagonist could be those who fear Naruto's new - found godlike powers. There might be ninja from other villages who see Naruto as a threat to the balance of power. Another could be remnants of Kaguya's old enemies who resurface, seeing Naruto as a continuation of Kaguya's influence and wanting to stop him. Also, there could be dark forces within the ninja world that want to corrupt Naruto's new powers for their own evil purposes.
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.
It could be some of the villagers who are jealous of Naruto's sudden growth under Shisui's training. They might try to undermine him or spread false rumors about him.
Well, it could be that Naruto, under Minato's training, quickly masters powerful jutsus. He might learn advanced space - time ninjutsu faster than in the original story. With Minato's guidance, Naruto could also develop unique combat strategies, making him seem godlike in battles against tough opponents like the Akatsuki members.
Maybe a powerful and corrupted Pokemon that has gained sentience and wants to rule both the Pokemon world and Naruto's world. It sees Naruto as an obstacle because of his godlike powers. This Pokemon could have the ability to control other Pokemon and use them to attack Naruto and those who oppose it. It would be a major antagonist as Naruto has to find a way to defeat it and restore peace to both worlds.
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.
Maybe there's a rogue ninja who has developed a new and dangerous jutsu that can counter Naruto's powers. This ninja wants to prove himself as the strongest by defeating Naruto and taking over the bijuu's power. He might be jealous of Naruto's newfound status and the respect he gets from the other ninjas.