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.
Maybe there could be a new group of villains emerging. They could be a secret organization that has been lurking in the shadows, and they see Naruto's new - found skills from Mangetsu's training as a disruption to their plans. They might target Naruto to prevent him from becoming too powerful and also to send a message to Mangetsu that they don't approve of his actions.
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 fanfic, perhaps Naruto is sent to the Hidden Mist for some sort of exchange program. There, Mangetsu takes him under his wing. Mangetsu might train Naruto not only in combat skills but also in stealth and strategy. Naruto, with his already strong will and determination, quickly adapts to Mangetsu's teachings and starts to combine his own Uzumaki - like chakra control with the water - style jutsu he learns, becoming a more versatile ninja.
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.
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.
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 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.
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.
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.
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 Otsutsuki clan members other than Kaguya could be antagonists. Since Kaguya is training Naruto, they might see Naruto as a threat to their plans.