Another possibility is that the main villain is a corrupted version of one of the characters from either universe. For example, a ninja who was influenced by the dark side of Hercules' world and now wants to rule with an iron fist. He would have the ninja skills along with some of the more brutal and power - hungry traits from Hercules' enemies.
Perhaps it could be a character who is jealous of both Naruto and Hercules. A sorcerer who was once shunned in both worlds and now wants to prove himself by defeating them. He could use dark magic to create chaos and try to stop Naruto and Hercules from uniting and using their combined powers.
It could be an evil ninja who has learned to use dark magic and wants to take over Pixie Hollow for its magic. He sees the fairies' magic as a source of power to enhance his own dark jutsu.
Another option could be Kabuto. He has been influenced by Orochimaru and is always looking for ways to gain more power. He might target Kurenai to learn more about her genjutsu and Naruto because of his status as a hero. Kabuto could be plotting to use their powers to further his own goals in the ninja world.
It could be Bowser who has somehow gained the power of a powerful ninja jutsu. He uses this new - found power to take over both the Mushroom Kingdom and start invading the Naruto world. His fire - breathing ability combined with ninja techniques would make him a formidable foe for Naruto and Mario.
It could be Orochimaru. Imagine he discovers the power of the ocean in Moana's world and wants to use it for his own dark experiments. He could start corrupting the sea creatures and causing chaos on Moana's island. Naruto, having faced Orochimaru before, would know his weaknesses and team up with Moana to stop him.
Perhaps a new character could be created as the main villain. This character could be an ancient being that was sealed away long ago and is now awakened by the interference of both Naruto's and Indiana Jones' worlds. The villain would be interested in using the unique aspects of both worlds, like Naruto's chakra and Indiana's artifacts, to reshape the universe according to his own desires. He would be extremely powerful, having abilities that neither Naruto nor Indiana has faced before, and would require them to combine their skills and knowledge in order to defeat him.
Perhaps a corrupted version of one of Naruto's comrades who has been influenced by the dark powers of Lucifer's world. This character would know all of Naruto's weaknesses and use them against him. At the same time, they would also have new demonic abilities, making them a formidable foe for both Naruto and Lucifer.
A likely main villain could be a new character, a powerful alien - ninja hybrid. This villain would have the ability to use both ninjutsu and advanced alien technology. He wants to rule both the Naruto universe and the Power Rangers SPD universe. He would be a formidable foe as he can use Naruto - like stealth and the high - tech weaponry of the SPD villains, forcing Naruto and the Rangers to really combine their skills to stop him.
It could be a powerful demon from the Inuyasha universe who has somehow managed to gain the ability to absorb the power of gods. This demon would see Thor as a prime target to drain his powers and use them to conquer both the Inuyasha world and potentially other realms. The demon's dark magic and newfound god - like powers would make it a formidable foe for Thor and Inuyasha's combined forces.
Hush could be an interesting choice. He could be spreading false rumors and causing distrust between the heroes and the citizens of both cities. His knowledge of Gotham's underworld and his ability to manipulate people could make him a formidable foe for Batwoman and Arrow. They would need to uncover his true identity and stop him before he completely destroys the relationship between the two cities.
Vilgax could be a great main villain. He has a long - standing rivalry with Ben and his presence would add a lot of tension. He could see Albedo as a useful tool or a threat depending on the situation. Another option could be an original villain created specifically for the crossover. Maybe a powerful alien entity that wants to use Albedo's knowledge and Ben's powers for its own evil purposes. A third choice could be Aggregor, who might be after some new power source that is related to both Albedo and Ben.