Maybe his special eyes allow him to see into the past. He could witness the great ninja wars as if he were there. This would help him understand the history of the ninja world better and gain wisdom from the past. He might see how his father, Minato, fought in the wars and learn new jutsu from those memories.
Another plot idea is that the special eyes can see through illusions that are normally undetectable. In a fight with Itachi, he could easily see through Tsukuyomi and other genjutsu. This would make him a formidable opponent against the Uchiha and those who rely on illusions.
One plot idea could be that Naruto's mystic eyes allow him to see the true nature of chakra. He can detect hidden traps or illusions that are based on chakra manipulation more easily. For example, in a battle against a powerful enemy who is skilled in genjutsu, his mystic eyes would give him an edge as he can see through the false chakra constructs of the genjutsu and counterattack swiftly.
One idea could be that Naruto's kids inherit his unique jutsu and struggle to master them while also dealing with the high expectations of being the Hokage's children. For example, they might have a hard time controlling the Nine - Tails' chakra like Naruto did at first.
The wings could also play a role in Naruto's relationship with other characters. For instance, Hinata might be in awe of his new appearance with wings. This could strengthen their bond. Or, some of his friends could be jealous of his new power. Naruto would then have to deal with these emotions while also trying to use his wings for the greater good. He could use them to quickly transport medical supplies during a war or to rescue hostages from a far - off location.
Another plot idea is that Naruto gets a Sharingan in a parallel universe. In this universe, he has to learn how to control it quickly while also dealing with the different political situations. Since the Sharingan is so powerful, many might try to either use Naruto or take the Sharingan from him, creating a lot of action - packed and suspenseful situations.
One plot idea could be that Naruto forgets all his ninja skills. So he has to start from scratch, relearning basic jutsus. This would be a great opportunity to show his determination as he struggles but still tries hard. Another could be that he forgets his friends, and his friends then have to make him remember them through shared memories and experiences. For example, Sasuke could tell Naruto about their battles and how they pushed each other to be better.
One plot idea could be Naruto discovers he has the Rinnegan during a particularly intense battle against a new, powerful enemy. His friends are initially shocked but quickly realize they need to adapt to this new power. Another idea is that the Rinnegan was secretly given to Naruto by an ancient entity as a last - ditch effort to save the ninja world from an impending doom that only Naruto can face with this power.
In some fanfics, Naruto's sibling could be a prodigy in a different area than Naruto. For example, while Naruto is good at combat and making friends, his sibling could be a master of stealth and espionage. Their different skills could lead to interesting team - ups or rivalries. Also, their relationship could be tested when the village's safety is at stake and they have different ways of handling the situation.
One plot idea could be that Naruto is influenced by a dark entity. Maybe an ancient evil spirit that latches onto him during a mission in a long - forgotten tomb. This spirit slowly corrupts his mind, making him see his friends as enemies. For example, he might start to believe that Sasuke is trying to steal his power, and so he begins to plot against Sasuke in a very un - Naruto - like way.
A really interesting plot could be that the Kyuubi bloodline in Naruto starts to have an effect on his relationships. Some people in the village might be afraid of him now that they know he has this powerful bloodline. On the other hand, some might see him as an even greater asset. Naruto then has to deal with the social implications while also training to control the new powers that come with his Kyuubi bloodline. He could also find out that there are other ninja out there with a similar bloodline from other tailed beasts, and they come together to form a unique group.
One possible story could be that Naruto's fox eyes give him a special ability to see in the dark. This helps him during his ninja missions, especially those at night. He can spot enemies lurking in the shadows more easily than his comrades.