Well, it could be that Naruto, being neglected in the village, is noticed by Shisui. Shisui sees Naruto's potential and decides to train him in stealth and combat skills. Naruto then starts to grow stronger under Shisui's guidance, and eventually surprises everyone in the village with his newfound abilities.
It could be some of the villagers who are jealous of Naruto's sudden growth under Shisui's training. They might try to undermine him or spread false rumors about him.
The Akatsuki could still be the main antagonists. Since Naruto is being trained by Shisui, they would see Naruto as an even greater threat. His new skills under Shisui's training could put their plans at risk. For example, if Naruto becomes better at stealth and infiltration, he could disrupt their operations more effectively.
One possible plot could be that Shisui imparts his unique Sharingan - related skills to Naruto. For example, he might teach Naruto how to predict opponents' moves better, just like how the Sharingan can analyze the flow of chakra and movements. This would give Naruto an edge in battles, especially against strong opponents who rely on speed and deception.
In a fanfiction where Naruto is trained by Shisui, it could change Naruto's whole ninja approach. Shisui was a very intelligent and skilled ninja. He could introduce Naruto to new forms of chakra control. This new training could make Naruto a more versatile fighter. For example, he might be able to combine his existing Rasengan techniques with the skills learned from Shisui, creating more powerful and unpredictable attacks. And Naruto's understanding of the ninja world and its politics might also be deepened through Shisui's teachings.
In this fanfiction, a really interesting plot twist could be that the training by Shisui actually awakens a dormant power within Naruto that has nothing to do with the Sharingan at first glance. As Naruto delves deeper into the Sharingan training, he starts to notice connections between this new power and the Sharingan. Maybe it's a power related to the Sage of Six Paths that gets activated in a unique way due to the Sharingan training. Also, the relationship between Naruto and Shisui could take an unexpected turn. Instead of just a teacher - student relationship, they could become something like comrades with a shared mission that is revealed during the training process.
Well, the plot could involve Naruto being overlooked in his own village, so he somehow ends up in the world of One Piece where Zoro takes him under his wing. Zoro might start training Naruto in his unique sword - fighting style, which Naruto could adapt to his own ninjutsu - based combat. For example, Naruto could learn to use his chakra to enhance the speed and power of sword strikes, similar to how he uses it for his shadow clones or rasengan.
In such a fanfiction, Naruto might become extremely powerful under Kakashi's training. He could learn new jutsus faster and gain better control over his chakra. Maybe he'd also develop a closer bond with Kakashi, different from his relationship with Iruka or other characters in the original story.
Naruto's character would likely become more serious and focused. Training with Shisui and the Sharingan would demand a lot of concentration, so he'd have to tone down his wilder side. He might also become more strategic in combat, as the Sharingan gives insights into opponents' moves.
Naruto would probably become more serious. Shisui was a serious - minded ninja. His training might make Naruto less impulsive and more calculated in his actions.