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.
In this fanfiction, Samus could be exploring a region where Pikachu are known to be very rare. She stumbles upon a small Pikachu that is injured. She takes it with her and nurses it back to health. As Pikachu recovers, they form a bond. When they discover that a powerful group is hunting Pikachu for their unique electric abilities, Samus and Pikachu fight together to protect the Pikachu population.
It could be a Pokemon itself. Maybe a dark - type Pokemon with a grudge against humans and Pikachu in particular. This Pokemon could be using its powers to cause chaos in the city, and Pikachu has to figure out its motives and stop it before it's too late.
It could be a new character, a powerful dark wizard who wants to use the combined power of Naruto's chakra and Pikachu's electricity for his own evil purposes. He creates all sorts of dark creatures and sends them after Naruto and Pikachu to try and capture them. He's very cunning and has a lot of minions to do his bidding.
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.
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.
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.
Obviously, the main characters are usually Pikachu. But sometimes, there could be other Pokémon that play important supporting roles. For instance, a Pichu could be a sidekick or a younger Pokémon that the Pikachus are protecting.
Well, clearly Raichu and Pikachu are the main characters. Sometimes, other Pokémon from their electric - type family or their friends like Ash might make an appearance in the background or play a minor role.