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 such a fanfic, Naruto might gain a whole new perspective on time and space from Barry Allen. Since Barry can manipulate time to an extent, Naruto could learn to anticipate his opponents' moves even better. Also, Naruto's chakra control could be improved in ways we can't even imagine. He might be able to use his chakra in a more efficient and powerful way, similar to how Barry uses the Speed Force. And the story could involve Naruto using his new - found abilities to protect the Hidden Leaf Village from threats that are beyond the normal ninja capabilities.
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 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.
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.
There might be some ancient forces or entities that are awakened by Naruto and Sasuke's new 'godlike' status. These could be demons or spirits that were sealed long ago and now see Naruto and Sasuke as threats to their plans of domination. They would be very powerful and require Naruto and Sasuke to use all of their enhanced abilities to defeat.
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.
Obviously, Naruto and Merlin are the main characters. Naruto is the one being trained, and Merlin is the trainer.
The main character is Naruto without a doubt. His journey of becoming godlike is the focus. The toads are also main characters. Big - name toads such as Fukasaku and Shima could be in it. They are likely to be the ones teaching Naruto. Their guidance and the bond between Naruto and the toads are important aspects of the story, making them all main characters in this fanfic.
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.