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.
One idea could be that Tinkerbell discovers a magical bubble that has the power to transport her to a new, enchanted world. There, she meets a unique character made of bubbles and they go on an adventure to save the bubble world from a dark force.
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.
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.
Mr. Sinister would be a great main villain. He's always had his own sinister plans for mutants. In a 'Termination' scenario, he could be taking advantage of the chaos to further his experiments on mutants, seeing it as an opportunity to create more powerful mutants under his control.
A new villain could be created specifically for this fanfiction. This villain could be a being that feeds on the chaos between the two different universes. It has the ability to disrupt chakra flow in Naruto's world and nullify magic in Lulu's world. Naruto and Lulu would have to figure out how to work together to stop this entity before it destroys both of their homes.
It could be a mad scientist. The scientist has been researching ways to combine organic and electrical energy. He sees Pikachu as the perfect specimen and Samus as someone who will try to stop his unethical experiments. So he sets out to capture Pikachu and eliminate Samus.
It could be a rogue shinobi who has found a way to enter the Matrix world and wants to take over both the real world and the Matrix. He uses his ninja techniques combined with the power of the Machines to create havoc.
Kabuto could also be a main villain in this context. He might see the potential in the gloves to further his own power - hungry goals. He could try to manipulate Naruto into using the gloves in a way that benefits him, or he could simply try to steal the gloves when Naruto is at his weakest.
It could be an evil ninja who has somehow gained access to Gem technology. He uses the power of the Gems to enhance his own jutsu and becomes extremely powerful. His goal could be to take over both the Naruto world and the world of the Gems.
Dr. Wily could be the main villain. He might have found a way to travel through time or dimensions to the world of Mega Man X. He then uses his knowledge of Mega Man's weaknesses and combines it with new technology in the Mega Man X world to create even more powerful and devious robots.