Sasuke could also be a top - tier character in a merged universe. His Sharingan gives him the ability to copy techniques and predict movements. In a world with the devils and other beings from Highschool DxD, he could use his Sharingan to analyze their powers and develop counter - strategies. His Rinnegan, if he has it in the fanfiction, could also give him access to extremely powerful abilities that could put him on par with the most powerful characters in the merged universe.
It's hard to say for sure, but Naruto himself could be a strong contender. His vast array of jutsu and his ability to grow in power constantly could make him extremely powerful. He has faced incredibly tough opponents and come out on top in the Naruto universe, so in a merged universe, he could use his skills to take on the devils and other beings.
It could be Issei if he were to gain Naruto's abilities. He already has his own set of powerful skills in the DxD world. Adding Naruto's chakra and jutsus like the Rasengan or the ability to summon toads would make him extremely formidable.
Probably Great Red from Highschool DxD. He's already an extremely powerful being in his own universe. If he were to encounter the power of the Omnitrix and all the alien forms in Ben 10, he could potentially assimilate or use those powers in some way to become even more powerful.
It's hard to say for sure, but some might argue that it could be Julius Novachrono from Black Clover. His time - magic is extremely powerful, and he could potentially manipulate time to his advantage in battles against the Highschool DxD characters. He could stop time and land fatal blows before his opponents even realize what's happening.
One way could be through a powerful magic - ninjutsu hybrid spell. Maybe a character with knowledge of both worlds accidentally creates a portal that merges the two. For example, if a shinobi in Naruto world somehow gets hold of a magic item from Highschool DxD and activates it in a wrong way.
Another approach could be a shared enemy. Suppose there is an entity that exists in both universes in a different form. Writers could create a story where the characters from Highschool DxD and Prototype have to team up to defeat this entity. This would require them to understand each other's powers and work together, leading to a lot of character development and exciting action scenes.
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.
One interesting crossover could be the sharing of combat techniques. For example, Naruto's shadow clone jutsu might be used in the Highschool DxD universe in a creative way during battles. It could help in confusing opponents just like how it does in the Naruto world.
One might argue that the Sage of Six Paths from Naruto would be the most powerful. He has the ability to create and shape the world. But in the context of a merged universe with World of Warcraft, the Lich King also has great power. He commands the undead and has powerful necromantic abilities. If they were to face off, the Sage of Six Paths' positive energy - based powers might be at odds with the Lich King's necromancy. It would be a battle of two very different but extremely powerful forces.
It could be Naruto. His ability to use chakra and his many powerful jutsu like the Rasengan and the Sage Mode would give him an edge. He also has great determination and a never - give - up attitude. He could probably adapt to the magic in the Harry Potter world quite well and use it in combination with his ninja skills.
It's hard to say for sure, but Naruto in his Sage of Six Paths mode is extremely powerful. However, Yuno from Future Diary has her own set of very deadly and unpredictable powers. If she were to target Naruto without him knowing, she could potentially be a huge threat. But Naruto also has the ability to sense danger and his large amount of chakra might give him an edge in a long - drawn - out battle.