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.
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.
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.
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.
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 has some hidden Senju abilities due to his relation to Hashirama. This could change the power dynamics in the ninja world. Maybe he could use Mokuton (Wood Style) more effectively than Yamato. Another twist might be in the political arena. His connection to Hashirama could make him a target or a key figure in disputes between different ninja clans. And it could also change his relationship with Sasuke, as Sasuke might view Naruto's newfound heritage in a different light.
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.
Maybe the ANBU who raise Naruto are actually part of a secret group within the ANBU that has its own agenda. They could be training Naruto to be a weapon against a hidden threat in the shinobi world. As a result, Naruto's journey would be about uncovering this conspiracy while also dealing with the fact that his upbringing has made him an outcast among the regular shinobi. For example, he might be too brutal in his fighting style for the more traditional ninja.
One possible plot twist could be that Naruto's values are very different from the original. Since he's raised by Female Madara, he might have a more aggressive approach to achieving peace. For example, he could be more willing to use forceful means rather than the diplomatic ways he often tries in the original story.
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.
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.