Perhaps an ancient evil spirit that was once sealed away in Moana's world. But due to some disturbance, it is awakened. This spirit has the power to control the elements and is attracted to the chakra in Naruto. It sees Naruto as a threat and tries to eliminate him while also causing destruction in Moana's world. Moana and Naruto would have to find a way to reseal the spirit.
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.
Obviously, Naruto and Moana would be the main characters. They are from their respective universes and would be the ones driving the story forward in a crossover. Their different personalities and abilities would create interesting interactions.
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 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.
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.
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.
The Reverse Flash could also be a main villain in this crossover. He travels to the Smallville universe to cause trouble. He might target Clark, thinking that by eliminating him early, he can change the future in his favor. This would force Barry and Clark to work together to stop the Reverse Flash's evil plans.
Kaguya could be a great main villain for this. Imagine Kaguya emerging on Halloween night, her already otherworldly appearance made even more menacing with spooky Halloween - like enhancements. She could use the energy of the night to her advantage, trying to plunge the world into eternal darkness, and Naruto and his friends have to stop her.
Kabuto could be a likely villain. He's very intelligent and has a thirst for power. He could use his knowledge of jutsu and his ability to manipulate others to try and steal The Flash's speed force. He might think that by combining it with his own powers and ninja techniques, he could become invincible.