Perhaps it could have a power of transformation. Not just in terms of its physical form, but also in how it affects Naruto. It could transform Naruto into a more spiritual - like being for a short time, granting him enhanced senses and the ability to interact with spiritual realms, which would be a very cool addition to his abilities in the fanfic.
Sukuna does die in the manga. The way it happens is quite dramatic and ties in with many other elements of the story, adding depth and tension to the overall narrative.
Maybe through some kind of special training or a unique ritual. It could be that he discovers a hidden method within the ancient scrolls of his village.
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.
In this fanfiction concept, Naruto's powers would be a blend of his own and what he could inherit from Itachi. Since Itachi was a very powerful ninja, Naruto might have an innate ability for genjutsu, which was one of Itachi's strong suits. His chakra control could be improved due to his Uchiha blood. And with the Sharingan, he might be able to use Susanoo in the future, although it would probably be a different form compared to Itachi's, as Naruto also has the Nine - Tails' chakra. This combination of powers would make him an extremely formidable ninja.
In a Naruto - Superman powers fanfic, perhaps Naruto gets some of Superman's powers accidentally. He struggles to control the new powers like heat vision and super speed along with his own ninja abilities. Superman, on the other hand, discovers he can use chakra in a limited way and they both have to figure out how to use these new combinations of powers effectively.
He could develop the ability to combine his chakra with Superman's powers. For example, he might be able to use his Rasengan while flying at super - speed. Or he could infuse his chakra into his heat vision to make it even more powerful.
In some Naruto fanfictions, Naruto's chaos powers might be shown as a wild and unpredictable energy source. It could make his jutsu more erratic but extremely powerful. For example, his Rasengan might become a chaotic, swirling mass of energy that can break through even the strongest defenses with ease.