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.
One interesting plotline could be Naruto having the power to control time. He could use this to prevent tragedies in the past, like the death of his parents. Another could be him having the ability to communicate with all animals, leading to new alliances and strategies in battles.
There are often super powers related to magical creatures in Harry Potter super powers fanfic. For instance, a character might have the ability to transform into a Phoenix at will, which would give them the power of rebirth and the ability to fly extremely fast. Another super power could be the gift of seeing the future with absolute clarity, not just in glimpses like Trelawney's prophecies but seeing entire timelines. And there could be a super power where a wizard can communicate with all magical plants and use them as allies, for example, making the Whomping Willow stop attacking or getting the Mandrakes to help in a fight.
He could have the power of energy absorption. So, when an enemy attacks him with a jutsu, he can absorb the energy and use it to strengthen his own attacks. It would be like a reverse - engineering of the attacks against him.
I really like 'Naruto's Superpowered Journey'. Here, Naruto is blessed with the power to understand and communicate with all living things. This power leads to some really interesting plot developments, such as him making alliances with normally hostile creatures in the Naruto universe. The story also delves into how Naruto uses this new power to bring peace to the ninja world in a different way than in the original series.
Super powers in fanfic can greatly change the original story. If a character has the power of instant healing, for example, many of the life - threatening situations in the original story would be easily resolved. This could change the relationships between characters as well. If Harry had a super power that made him invincible, Voldemort would have a much harder time trying to kill him, and the whole dynamic of their struggle would be different.
In this fanfiction, the prototype powers could be something like an early form of chakra manipulation that is different from the traditional Naruto world's chakra use. It might be more raw and unrefined, with the potential for new and unique jutsu.
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.
Imagine Naruto with all those alien fanfic powers. He could have the power of super strength like some hulking alien species, or the ability to turn invisible like certain stealthy aliens. His combat style would be a wild mix of ninja techniques and alien powers. He could shoot energy beams from his hands or teleport across long distances without using ninja techniques. This would make him a force to be reckoned with not only in his own world but potentially across the universe in a much broader sense.