Well, Naruto could become a more stealthy fighter. With Rogue's powers, he might be able to absorb the chakra or abilities of his opponents, which would give him a huge advantage in battles. He could also use Rogue's power - related to stealth and misdirection - to infiltrate enemy bases more easily.
He'd become more complex. Naruto is already a determined character, but with Rogue's powers, he'd have to deal with the moral implications of absorbing others' powers. This would add depth to his character.
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, Rogue's power to absorb the powers and memories of others and Spiderman's spider - like abilities could create some interesting scenarios. If Rogue absorbs Spiderman's powers, she might be able to use his spider - sense in a more instinctual way than he does. On the other hand, Spiderman could learn from Rogue how to better control his powers when she has absorbed some of his essence. Their powers could also be used in combat in a more coordinated way, like Spiderman creating webs for Rogue to swing on while she uses her absorbed strength to take down enemies.
His hidden powers might be the ability to control all five basic nature types without any training. In the original story, Naruto had to work hard to master different nature types. But in a fanfiction, it could be that he has this innate ability which was hidden all along. This would make him extremely powerful and feared by his enemies.
In some fanfictions, Naruto's multiverse powers are portrayed as a way to bring together different versions of himself. Each version has its own set of skills and knowledge. By merging these aspects, he becomes an even more powerful and complex character, able to solve problems that were previously insurmountable.
Naruto's character development would likely be a wild ride. Bill Cipher's powers are extremely powerful and otherworldly. Naruto could start to see the world in a different light. He may become more detached from the normal ninja way as he explores the limits of his new powers. This could lead to some conflicts with his friends, as they might not understand the new Naruto who has these strange and dangerous powers. He might also gain a new sense of arrogance at first, thinking he can solve all problems with his newfound abilities, but then have to learn humility through some tough experiences.
Well, Naruto would probably become more confident. With all those devil fruit powers, he could be even more fearless in battles. He might start to rely less on his original ninja skills and more on the unique abilities from the devil fruits, which could change his fighting style drastically.
His prototype powers could make others either fear or envy him. Some might see him as a threat due to his new and untested abilities. For example, villagers who were already suspicious of Naruto because of the Nine - Tailed Fox might be even more wary.
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.