Sasuke could also be a top contender. His Sharingan and Rinnegan abilities are extremely powerful. In the combined universe, he could study the yokai and find ways to use their weaknesses against them or even gain some of their powers. His thirst for power would drive him to constantly improve and adapt, making him a force to be reckoned with.
Rikuo Nura from Nura Rise of the Yokai Clan has a strong claim. He is the leader of the Nura clan and has both yokai and human forms. His yokai powers are vast, and if he were to gain some ninja skills from the Naruto universe, he could be nearly unstoppable. He has the ability to command a large number of yokai, which is a great asset in any battle.
Rikuo Nura is a great character to write about. His dual nature as a human during the day and a yokai leader at night provides a lot of room for character development. You can explore his struggles to balance these two identities and how he deals with the expectations of both the human and yokai worlds.
A great crossover could involve the sharing of powers. For example, a character from Naruto might gain some yokai - like abilities from the Nura world and vice versa. This could lead to some really cool fight scenes and character development. Maybe Naruto himself could learn some yokai magic and use it in his battles, creating a whole new fighting style.
One interesting plot idea could be a crossover where Naruto characters end up in the Nura world. They could team up with the Nura clan to fight a common enemy that threatens both their realms. For example, an ancient evil that can manipulate chakra and yokai energy.
Kurotabo is quite an underrated character. He is very loyal to the Nura Clan and has his own set of skills. Fanfiction could focus on his past and how he developed his loyalty to the Nura family.
For a crossover with a mecha anime, Kubinashi could be a key character. His skeletal form and his skills could be used in piloting or modifying mechas. And for a crossover with a ghost - hunting series, Nurarihyon, with his vast experience and power, could lead the team in dealing with both yokai and other supernatural entities.
It could be Naruto himself. With his already powerful ninjutsu and the potential to gain Fairy Tail magic, he would be extremely formidable. His ability to quickly learn new skills and his large chakra reserve, combined with something like Fairy Tail's celestial magic, would make him a force to be reckoned with.
One idea could be exploring the backstory of some minor yokai characters in more detail. For example, you could write about how a certain yokai came to be part of the Nura Clan.
It could be Naruto himself. He has an enormous amount of Chakra and his ability to learn new techniques quickly. If he were to partner with a powerful Digimon like Omnimon, he would be nearly unstoppable. His ninja skills combined with Omnimon's power would make him a force to be reckoned with.
I think it could be a combined form of a character. For example, if Issei were to somehow gain the power of the Nine - Tailed Fox. He already has his Boosted Gear and his experience in battles in the Highschool DxD world. Adding the Nine - Tailed Fox's chakra would make him an extremely formidable opponent. He could use the fox's chakra to enhance his Sacred Gear even further, and his new form might have abilities that are a combination of both universes, like using the fox's tails as a weapon while also having the power of the Boosted Gear.
The complex hierarchy within the yokai clans can be a great aspect to explore. You could write about power struggles, alliances, and betrayals among different levels of yokai. For instance, a lower - ranked yokai trying to rise in the ranks by outsmarting the higher - ups.