A powerful demon from Naruto's world could be the main villain. It gets lured to Pixie Hollow by the pure magic there. It wants to consume all the magic and turn Pixie Hollow into a dark place. Naruto and Tinkerbell would have to put aside their differences and use their combined skills to stop this demon.
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.
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.
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.
If it's a crossover with Alice in Wonderland, the Queen of Hearts could be the main antagonist. The Queen might see Tinkerbell as an intruder and try to behead her. Tinkerbell would have to use her wits and magic to survive in the crazy world ruled by the Queen of Hearts.
A group of mischievous imps could be the villains. They are envious of the beautiful things that Tinkerbell and the bubble can create together. So they play tricks on them, like creating false illusions to make Tinkerbell doubt the bubble and vice versa. Their goal is to disrupt the harmony between Tinkerbell and the bubble so that they can't use their combined magic for good in the fairy world.
A powerful demon lord from the underworld could be the main villain. This demon lord could be seeking to expand his territory into the Naruto world, using his dark magic and hordes of minions.