In such a fanfiction, perhaps Minato passes on his own unrivaled speed techniques to Naruto more effectively. Naruto, being a quick learner as he is, combines these with his already existing Rasengan skills. This could lead to him creating new and more powerful versions of the Rasengan, which in turn makes him appear godlike in combat situations. Also, Minato might train Naruto in the art of stealth and surprise attacks, something Naruto wasn't as good at before.
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.
One possible plot could be that Naruto, under Kaguya's training, gains godlike powers at an accelerated rate. He might learn ancient and powerful jutsu that were once exclusive to Kaguya. This could lead to him facing new and extremely powerful enemies, perhaps even threats from other dimensions. With Kaguya's guidance, Naruto could also gain a deeper understanding of the chakra and its origins, and use this knowledge to reshape the ninja world for the better.
One possible plot could be that Naruto, seeking to gain new powers, somehow ends up in Ichigo's world. Ichigo, seeing Naruto's potential, decides to train him. Naruto then has to adapt to Ichigo's training methods which are different from what he's used to in Konoha. As he trains, he starts to combine his ninja techniques with Ichigo's Soul Reaper powers, becoming a truly godlike figure.
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.
Well, in such a fanfiction, it might be that Naruto becomes extremely powerful like a god. Since he is trained by the Kyuubi, he could gain unique powers and abilities. Maybe he masters the Kyuubi's chakra in ways no one else has. He could use this power to defeat powerful enemies, protect his village in extraordinary ways, and perhaps change the entire shinobi world with his new - found god - like strength.
In this fanfic, perhaps Naruto's godlike powers would be a result of Danzo's unorthodox training methods. Danzo could push Naruto to his limits, making him a force to be reckoned with. Naruto might also have to deal with the distrust of his friends at first, as they are suspicious of his association with Danzo.
In this fanfic, perhaps Deadpool's training makes Naruto question his own beliefs and values. Naruto has always been about friendship and protecting the village, but Deadpool's chaotic nature might make him see things from a different perspective. As Naruto becomes more 'godlike', he has to balance his newfound power with his original ideals, and this internal struggle could be a major part of the story.
Well, perhaps Naruto, with his natural talent, is taken under Merlin's wing. Merlin could teach Naruto some really powerful magic or unique combat strategies. Maybe Naruto becomes even more powerful than in the original series and uses his new skills to protect his village in ways no one expected.
One possible reason could be fear. If Naruto was 'godlike' in this fanfiction, his power might be uncontrollable and Minato, as Hokage, might feel it's a threat to the village. He could think that Naruto's power could attract too many dangerous enemies or cause destruction accidentally.
The plot might start with Naruto being chosen by some sort of ancient power or prophecy to be trained by Hashirama. During the training, Naruto would face various challenges. He could struggle with adapting to Hashirama's old - fashioned training methods at first. But as time goes on, he would start to master skills like summoning giant wooden golems and using the life - force of plants to heal himself and others. This newfound power would put him in a position to reshape the ninja world for the better.
In such a fanfiction, Naruto could gain unique powers. Shendu, being a powerful and often devious entity, might train Naruto in unorthodox ways. Naruto could learn new combat styles and perhaps some dark or ancient techniques. This would likely put him at odds with his usual ninja values at first, but he'd probably find a way to blend the new knowledge with his own beliefs to become an even more formidable shinobi.