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.
Maybe Mikoto is training Naruto in secret because she has foreseen a future where only he can save the Uchiha clan. So she's teaching him Uchiha techniques that no one outside the clan has ever known, which would lead to a lot of shock and intrigue when revealed.
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 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.
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 twist could be that Yugau Uzuki has a secret jutsu that she passes on to Naruto which changes the way he approaches battles. For example, it could be a space - time related jutsu that allows him to surprise his opponents. Another twist might be that Jiraiya discovers a hidden power within Naruto that is related to an ancient prophecy that neither of them were aware of before. This could lead Naruto on a new quest to understand and master this power.
A plot twist could be that Naruto and Mikoto are forced into a political marriage. They initially don't get along but as they face various challenges together, they start to fall in love. For example, they might have to deal with other ninja villages trying to undermine their union. Also, there could be a twist where Mikoto loses her memories and Naruto has to make her fall in love with him all over again while also preparing for the wedding.
One possible plot twist could be that Naruto, despite being trained by Shisui and Itachi, struggles with the darker aspects of their teachings. For example, he might find it hard to adapt to their more stealthy and sometimes morally ambiguous tactics. Another twist could be that an enemy figures out Naruto's new training sources and uses it against him by setting traps based on the Uchiha's fighting styles. Also, Naruto could discover a hidden connection between the Uchiha clan and his own Uzumaki heritage during the training process that changes his perspective on his powers and destiny.