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.
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.
Well, he could use Freddy's power of entering people's dreams to fight his opponents in the dream realm. Maybe he would trap his enemies in a never - ending nightmare, causing them mental distress and weakening their will to fight in the real world.
He could have enhanced physical abilities. Since yokai are often known for their strength and speed, as the King of Yokai, Naruto might gain even greater strength and faster reflexes. He may also have the ability to communicate with all types of yokai, understanding their languages and thoughts, which would give him an edge in dealing with them.
Well, Naruto would become extremely powerful. He could use Sinbad's magic powers along with his own ninja skills. Maybe he could fly around the Hidden Leaf Village like Sinbad on his magic carpet and use his powers to protect the village in ways he couldn't before. It would be a really cool combination.
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.
In some fanfictions, Naruto might gain the ability to control energy like a laser beam which is an alien - like power. For example, he could shoot beams from his hands to defeat enemies.
There are likely fanfictions where Naruto's immortality in the Fairy Tail setting gives him unique powers. For example, he might be able to combine his ninja skills with Fairy Tail magic in ways that no one else can. His immortality could also mean he has an infinite amount of time to master different types of magic, making him an extremely powerful and feared figure in the Fairy Tail world.
One potential consequence could be a shift in the power balance. Naruto was already a strong force, but with Akatsuki powers, he could become nearly unbeatable. This might make other villages either fear him or try to ally with him more strongly. Enemies of Konoha might think twice before attacking. Also, the Akatsuki's powers often come with a certain darkness, so Naruto might have to struggle with that aspect of his new abilities.