One possible plot twist could be that Tsunade trains Naruto not just in physical combat like she did with others, but also in medical ninjutsu. This would be unexpected as Naruto is more known for his brute force. Maybe Naruto uses his new medical skills in a creative way during a battle, like healing his opponents to show mercy and then defeating them when they are off - guard.
A plot twist could be that Slade has an ulterior motive for training Naruto. Maybe he plans to use Naruto as a weapon against Konoha in the future. He might be secretly feeding information about the village's defenses to an enemy while training Naruto. So, when Naruto discovers this, he has to find a way to stop Slade and also deal with the fact that he has been unknowingly part of a scheme against his own home.
One possible plot twist could be that Mikoto discovers Naruto has a hidden kekkei genkai that she helps him unlock. This new power could completely change Naruto's abilities and how he's perceived in the ninja world.
One possible plot twist could be that Sakumo's training methods are very unorthodox compared to what Naruto is used to in the village. For example, he might focus more on stealth and assassination skills which Naruto initially struggles with as he is more used to head - on combat. Another twist could be that Sakumo has a hidden agenda for training Naruto, like he is preparing Naruto for a specific threat that he foresees but hasn't shared with the village yet.
Another plot twist could be that the situation Tsunade is in is actually a trap set by an enemy to lure Naruto in. So, while Naruto is trying to save Tsunade, he has to also deal with the real mastermind behind the whole thing. This would add an extra layer of complexity to the story.
A plot twist could be that Urahara's training makes Naruto lose his ability to use shadow clones for a while. This forces Naruto to rely on other skills he's learned from Urahara, like swordsmanship or some new type of jutsu. It would also make his friends and enemies question his power and how to deal with this new Naruto.
One possible plot twist could be that Zabuza's training methods lead Naruto to develop a darker side. Naruto might start to question his own values as Zabuza's more ruthless ways of fighting seep into his mindset. For example, he could become more willing to use underhanded tactics in battles, which would shock his friends.
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.
Another plot twist could be that Obito is secretly training Naruto to fight against an even greater enemy that no one else is aware of yet. This enemy could be an ancient force that is about to awaken, and Obito believes Naruto is the only one who can stop it. So, he's training Naruto in unique and unorthodox ways that seem strange to others at first.
One possible plot could be that the female Naruto has to overcome the initial disbelief and discrimination within the village. Tsunade, seeing her potential, takes her under her wing. She trains her not only in physical combat like the Rasengan but also in medical ninjutsu. As she grows stronger, she faces off against new threats to the village, using her unique combination of skills learned from Tsunade and her own natural tenacity. Eventually, she earns the respect of the entire village and becomes a great ninja like her male counterpart was in the original series.
One possible plot twist could be that Naruto develops a different fighting style. Since Tsunade is strong in physical combat and medical ninjutsu, and Jiraiya is a master of various ninjutsu and toad summons, Naruto might combine their teachings in unique ways. For example, he could use medical ninjutsu to enhance his own physical abilities during combat, similar to how Tsunade uses her strength. Another plot twist could be in his relationships. With Tsunade and Jiraiya as his guardians, he might have a different attitude towards the Hidden Leaf Village's elders. He could be more critical or more understanding depending on how they've influenced him. Also, his training might be more focused on stealth and intelligence gathering, skills that Jiraiya was good at, rather than just brute strength.