Well, his super powers might make him a target at first. People could be either jealous or scared of him. So he might have a hard time making friends. He'd also probably attract the wrong kind of attention from some villains who want to use his powers for their own evil plans.
If Naruto was born in the Uchiha clan in fanfiction, he would surely have the Sharingan. This powerful eye technique would give him enhanced perception, allowing him to copy other ninja's moves more easily. He could also use Genjutsu more effectively. Along with that, he might still have some connection to the Nine - Tails, but it could be more subdued or combined with his Uchiha powers in a unique way. Maybe he could use the Nine - Tails' chakra to boost his Sharingan abilities, like increasing the power of his Amaterasu if he were to unlock it.
He might have powers like shape - shifting into a more demonic form. Maybe he could have the ability to breathe fire or some other elemental powers related to chaos or destruction. He could also have enhanced strength and speed that are far beyond what a normal ninja has, and his senses could be super - sharp to detect danger or prey.
One possible power could be instant teleportation within a certain range. Some sage - like abilities in Naruto involve quick movement between spaces. Naruto, as a born sage, could use this to surprise his enemies in battle. He could suddenly appear behind an opponent or quickly move to a strategic location, giving him an edge in combat.
Often, Orochimaru remains an antagonist even in these fanfictions. His thirst for power and immortality makes him a natural foe for Naruto, especially when Naruto has new super powers to protect. Another common one could be Madara Uchiha, as his grand plans for the world are likely to clash with Naruto's newfound abilities and his desire to protect peace.
Some fanfictions have Naruto getting super powers as a result of a divine intervention. Maybe the gods or goddesses of the Naruto universe see his great potential and decide to give him additional powers to help him in his quest to bring peace. This can lead to all sorts of interesting plot developments, like him having to prove himself worthy of these powers to the divine beings or facing the envy of other ninjas who don't have such divine blessings.
He could develop enhanced hearing powers. Similar to how some real - world blind people have extremely acute hearing, Naruto could use this to detect enemies from afar. He might also be able to sense the flow of chakra in a more detailed way. For example, he could sense the different types of chakra in a person's body just by being close to them. Another power could be the ability to echolocate, like some animals do. By emitting chakra in a certain way and listening to how it bounces back, he could create a mental map of his surroundings.
Well, Naruto could develop some really cool powers. Since natural chakra is related to nature itself, he might be able to communicate with animals on a deeper level, like the Sages can. He could also gain the ability to manipulate plants, for example, make vines grow rapidly to entangle his enemies. And his Rasengan could be infused with natural chakra, making it much more powerful and having additional effects like causing a shockwave of natural energy that can stun opponents.
Well, Naruto's chakra - based powers could be quite unique in the Marvel Universe. His ability to use ninjutsu like the Rasengan could be seen as a very specialized form of energy projection. Maybe it would be considered a mutant - like power, or something completely new that S.H.I.E.L.D. would be very interested in studying. He could also use his shadow clone jutsu to outnumber his opponents, which would be a great advantage in battles against Marvel villains.