It could be an evil wizard from Harry's world who has found a way to cross over into the Rescue Rangers' realm and wants to take it over. He might see the Rangers as easy targets at first, but then realizes Harry is there to stop him.
A dark entity that feeds on the chaos between the two different worlds. It manipulates events in both Harry's world and the Rescue Rangers' world to create more chaos so it can grow stronger. It disguises itself and plays on the fears and weaknesses of the characters, trying to turn them against each other before they figure out its true identity and try to stop it.
Maybe a powerful and corrupt inventor in the Rescue Rangers' world. This inventor creates dangerous machines and has a grudge against both the Rangers and anyone from other worlds like Harry. He wants to use his inventions to rule both worlds and will stop at nothing to achieve his goal. He could be constantly devising new traps and weapons to defeat Harry and the Rescue Rangers.
It could be a greedy land developer. He has plans to build a huge shopping mall on the land where the Dalmatians and their owners live. In order to clear the land, he decides to get rid of all the animals, especially the Dalmatians puppies which he sees as a nuisance. He sets traps and hires people to capture the puppies, making him a very menacing villain in the fanfiction.
It could be a new character that is a combination of a dark wizard and a Hollow. This creature would be able to use both dark magic and Hollow abilities. It would target both Hogwarts students and Soul Reapers. Ichigo and Harry would have to figure out its weaknesses, which would be a difficult task as it has powers from two very different universes.
One idea could be that Harry gets lost in the Rescue Rangers' world and they have to help him find his way back home. Another could be that the Rescue Rangers need Harry's special skills, like his magic if he has any in this fanfic, to defeat a powerful villain that has emerged in their world. Maybe Harry teams up with the Rangers to rescue a group of magical creatures that are being held captive by an evil force.
Voldemort could still be the main villain in a different way. Suppose he discovers Tonks' unique connection to Harry and tries to use her as a weapon against him. He could manipulate her mind or put her in dangerous situations to force Harry to make sacrifices or bad decisions.
It could be a new dark wizard who has been secretly plotting in the shadows. This wizard might be jealous of Harry's fame and power, and decides to make him disappear so that he can rise to power unopposed. He could have a group of followers who are experts in dark magic and are able to carry out his plan to make Harry vanish.
The Queen of Hearts would make a great main villain. Her tyrannical rule and quick temper in the original Wonderland story could be amplified in a fanfiction. She could be a powerful dark magic user who sees Harry as a threat to her rule and tries to stop him from achieving his goals in Wonderland.
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 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.