Well, it could be that Naruto's relationship with the other Konoha ninjas changes drastically. They might see him as an outcast because of his association with Kisame. On the other hand, Naruto might try to bridge the gap between Konoha and the Akatsuki due to his upbringing by Kisame. This would create a whole new set of conflicts and alliances within the Naruto universe.
One possible plot twist could be that Naruto develops a much darker and more ruthless side due to Zabuza's influence. Instead of the optimistic and friendly Naruto we know, he might be more solitary and calculating in his approach to battles and relationships. For example, he could be more willing to use underhanded tactics like Zabuza's use of hidden mist jutsu to ambush opponents.
One possible plot twist could be that Naruto inherits Hashirama's unique Wood Style jutsu much earlier and in a more powerful form. Since Hashirama was a master of this powerful ability, he might train Naruto intensively in it. This would make Naruto stand out even more in the ninja world and perhaps change the way his peers and enemies view him.
One possible plot twist could be that Naruto gains unique fire - related powers from the phoenix. Since the phoenix is often associated with fire in many mythologies, Naruto might be able to control a different kind of fire jutsu, which would set him apart from his normal abilities in the original Naruto story.
Perhaps Naruto's relationship with the other ninja in Konoha is affected. Since Yoruichi has a different set of values and skills compared to the traditional Konoha ninja, Naruto could be seen as an outlier. This could lead to some initial misunderstandings and later, a new form of respect from his peers as they see the effectiveness of his unique upbringing.
Perhaps Naruto discovers that Kisame has a family he's been protecting in secret, and this new knowledge makes Naruto see Kisame in a different light. He then tries to help Kisame reunite with his family while also dealing with the Akatsuki.
A plot twist could be that Koharu has a connection to an ancient and powerful jutsu that she passes on to Naruto. However, this jutsu comes with a dark side or a price. Naruto then has to struggle with using this power for good while also dealing with the negative consequences it brings. He might have to make some difficult moral choices that test his character in ways he hasn't been tested before.
One possible plot twist could be that Naruto's Mokuton abilities attract the attention of Orochimaru. He might try to capture Naruto to study his unique power. Since Tsunade raised Naruto, she would be extremely protective and engage in a fierce battle with Orochimaru to keep Naruto safe. This would not only test Tsunade's strength but also Naruto's growth under her care.
Perhaps the Hyuga clan's strict traditions and Naruto's more free - spirited nature clash. This could create internal conflicts within the clan as some members see Naruto as a threat to their way of life, while others see him as a new opportunity for the clan to grow. For example, Naruto might want to teach the younger Hyuga members some of his unorthodox ninja skills, which could be met with resistance from the more conservative elders.
Well, a really interesting plot twist might be that Naruto's upbringing among the Uchiha makes him question his own identity more than in the original story. He might be torn between his Uzumaki heritage and the Uchiha values he was raised with. For example, the Uchiha are known for their pride and a certain sense of isolation in some ways. Naruto, with his usual sunny disposition, could either rebel against these aspects or try to find a new way to incorporate them into his life. This internal conflict could lead to some really intense character development and might even change the way he approaches his relationships with other characters like Sasuke. Maybe he'd understand Sasuke's actions from a different perspective, which could completely shift the dynamic of their relationship.
Another plot twist might be in Naruto's relationships. With Konan as his caregiver, he could have a different dynamic with the other Akatsuki members. For example, he might form an unexpected bond with Pain. Konan could act as a mediator between Naruto and Pain, leading to a situation where Naruto tries to understand Pain's ideology from a different perspective.