One possible plot twist could be that Danzo, despite being 'good', has a hidden agenda related to Naruto's power. Maybe he wants to use Naruto to gain political influence in the Hidden Leaf. Another twist could be that Naruto discovers Danzo's past misdeeds while being trained, which creates a moral dilemma for him. He has to decide whether to continue training under someone with a dark history or break away.
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.
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, if Naruto was trained by Danzo, he might be more ruthless at first. But joining Team 7 could soften him up. He'd probably bring some of Danzo's combat techniques and secrecy to the team. It could make for an interesting dynamic, with Naruto being a bit more of an enigma compared to his canon self.
Naruto might become more calculating. Since Danzo is known for his strategic thinking, Naruto could pick up on that. He may not be as impulsive as in the original story.
In such a fanfiction, Naruto might become a more shadowy and ruthless ninja. Danzo's training methods are often extreme and focused on loyalty to the village above all else. Naruto could lose some of his idealism and become more of a tool for Danzo's political games.
Well, if Naruto was trained by Danzo in fanfiction, it would be a huge departure from his normal growth. Naruto is all about hope and friendship. But under Danzo's tutelage, he could be molded into a more cynical shinobi. His jutsu might develop in different directions. For example, he could be pushed to learn more dangerous and morally ambiguous ninjutsu. Also, his relationships with his friends might change as he becomes more secretive and less open - hearted due to Danzo's influence.
If Naruto was trained by Danzo and joined Team 7 in a fanfic, his abilities would change significantly. Danzo's training would probably give him a more strategic mindset. He could be more proficient in using weapons and stealth. In Team 7, he'd learn to coordinate with Sasuke and Sakura. His chakra control might improve in different ways, and he could develop new jutsu that are a combination of what he learned from Danzo and what he discovers while on missions with Team 7.
Naruto's character would likely become more reserved. Danzo's training might make him less trusting. He would probably be more calculating in his actions, weighing the benefits for the village more strictly. He might also be more inclined to use force or manipulation to achieve his goals, which is quite different from his original self.