It could be an evil version of the Sage of Six Paths. He might want to take the Juubi's power from Naruto for his own dark purposes.
It could be a powerful ninja from Naruto's world who has been corrupted by the Juubi's power and somehow ended up in the Inuyasha world. He wants to use the power of the demons in the Inuyasha world to make himself even stronger and take over both worlds.
Madara Uchiha could be a great antagonist in this fanfic. Even though he was defeated in the original Naruto story, if he somehow gets resurrected and gets a chance to control the Juubi, he would be a formidable foe. He already had grand plans for the world in the original story, and with the Juubi's power, he could be even more dangerous. He might want to reshape the world according to his vision, and Naruto would have to fight him once again to protect everyone.
Perhaps a rogue Sekirei who has been corrupted by the power of the Juubi's energy that has seeped into the Sekirei world. This Sekirei could start causing chaos, believing that they are now more powerful than the others and should rule over them. Naruto would then have to stop this Sekirei from causing more destruction and bring balance back to the Sekirei world.
In the 'naruto juubi alternate universe fanfiction', it would be interesting if the characters' relationships were reversed. Like Sasuke could be the one trying to protect Naruto who has the Juubi's power, because he realizes that Naruto's power is the key to a new world order that could benefit all ninjas.
The fanfiction could change the Naruto universe by introducing new threats. With Naruto so powerful, there could be forces that emerge to try and counterbalance his strength. Also, the story could explore different ways of using chakra, as Naruto's merged state might have unique chakra abilities. It could also affect the way ninjas are trained, as they might try to achieve a similar level of power.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
He could meet alternate versions of his friends. For instance, an alternate Sasuke who has never left the village and is a strong ally from the start. This Sasuke could be more open and friendly, and together they could face the challenges of the new universe.
Obviously Naruto and Korra could be main characters. Naruto with his experience with the tailed beasts would be crucial in dealing with the Juubi. Korra, as the Avatar, has the power to bend all four elements and could use her abilities in new and creative ways to fight against the Juubi.
Obviously Naruto is one of the main characters. Given the title, he has a significant connection to the Juubi in this fanfiction.
Maybe a new character could be introduced as the main antagonist. This character could be from a hidden village that has been secretly observing Naruto's growth. They realize his potential as a weapon and plan to steal his power or use him to start a war against other villages.