He might face anti - ghoul organizations. Just like in the Tokyo Ghoul universe, there could be groups dedicated to eradicating ghouls. These groups would see Naruto as a threat even if he was trying to use his powers for good. He could also face other ghouls who are jealous of his unique situation, being a ninja with ghoul powers. They might try to either recruit him or eliminate him.
Naruto could face enemies created by those who fear his power. For example, a group of rogue ninja scientists might create super - powered clones or monsters designed to take him down. Also, there could be alien threats similar to the ones Superman faces in his universe. Since Naruto now has Superman - like abilities, he would be on the radar of intergalactic villains. And there might be dark versions of himself, created by dark magic or some evil jutsu, that have the same powers but an evil intent.
If Naruto had ghoul powers in fanfiction, it would change the story drastically. For one, his combat style would be very different. Ghoul powers involve using kagune, which are like weapons made from the ghoul's body. Naruto's usual ninjutsu and shadow clone jutsu would be combined with these new powers. He might be able to use his chakra to enhance his kagune attacks. Also, his relationship with his friends could change. Some might be afraid of his new, more monstrous side. And his role in the ninja world would shift as he'd have to hide his ghoul nature from those who would hunt him if they knew.
Another ability could be dark energy projection. Naruto could project bolts of dark energy from his hands or body. This energy could be used to blast away enemies or even to corrupt other things it touches, like sealing jutsu or barriers. It would be a very different and more sinister form of attack compared to his normal Rasengan.
Well, Naruto could gain the ability to heal in a more advanced way. Just as the avatar can sometimes use their connection to the elements to heal, Naruto might be able to do the same with his chakra. He could also have the power to merge with the natural world around him, similar to how the avatar can connect with nature. This would give him an edge in stealth and surprise attacks. Plus, he could develop a new form of sensing, being able to detect not just chakra but also the energy of the elements around him.
In the fanfiction where Naruto has Bill Cipher's powers, he'd face some really tough challenges. He would struggle with the fact that his powers are so different from what he's known all his life. His normal training methods may not work to improve or control these powers. There could be a lot of collateral damage when he first starts using them, which would make people angry and afraid of him. Moreover, he might attract the attention of some really powerful and evil forces who would either want to steal his powers or use him for their own malicious purposes. And on a personal level, Naruto might start to question his own identity as a ninja and a person, as these new powers could make him feel like he's becoming something he doesn't fully understand.
Maybe he has the power of a different tailed beast. Since Naruto has a connection with the Nine - Tailed Fox, his son could be linked to another tailed beast, which would give him a whole new set of powers and challenges. He'd have to learn to control this power, just like Naruto did with the Nine - Tailed Fox's chakra.
Naruto could potentially gain allies among the water - based creatures in the Naruto universe. With the trident, he could communicate or form a bond with them. However, he might also draw the ire of those who oppose any form of outside power or interference. There could be ninja clans or groups that believe Naruto having a weapon from another mythology is against the natural order of the ninja world. This could lead to new enemies who would stop at nothing to get rid of Naruto and the trident.
One new ability could be the power to charge his own body with kinetic energy for enhanced physical attacks. He could deliver punches or kicks that explode on contact, similar to Gambit's charged staff strikes. Another ability would be to create energy barriers by rapidly charging the air around him. This would be a great defensive move, something Naruto currently lacks in his regular skill set. He could also potentially use Gambit's power to sense the energy levels of his enemies from a distance, giving him an advantage in strategizing his attacks.
He might gain an enhanced sense of smell that could help him track enemies over long distances. Just like Wolverine can smell fear or detect the presence of people from far away, Naruto could use this to his advantage in finding missing - nin or locating hidden bases. Also, his balance and reflexes could be improved. Wolverine has amazing reflexes, and Naruto would inherit that, making it harder for enemies to land a hit on him during battles.
Well, Naruto would become an even more formidable fighter. He could stretch his limbs like Luffy, which would add a whole new dimension to his combat style. He could reach enemies from a distance, or use his stretching abilities for quick evasions. This would make his already impressive ninja skills even more unpredictable and powerful.