Green Goblin might be interested in the magic of the wizarding world. He could fly to Hogwarts and start stealing magical artifacts. Harry Potter and Spider - Man would need to join forces to stop him from using these artifacts for evil. He could use his glider and pumpkin bombs in the wizarding world, causing a lot of chaos.
Voldemort could be a great villain. Imagine him getting his hands on some of Spider - Man's technology. He could use it to enhance his Death Eaters' powers or even create new, more powerful dark magic. Spider - Man and Harry would have to put aside their differences in fighting styles and worlds to stop him.
The Green Goblin could be a likely villain. His chaotic nature and powerful glider - based attacks would pose a great threat to both Wonder Woman and Spider - Man. He could be after some sort of powerful artifact that Wonder Woman has knowledge of, and Spider - Man gets involved trying to stop him from getting it.
Another possible villain could be Fenrir Greyback. He is a werewolf in the Harry Potter world, and Wolverine also has some werewolf - like qualities. Fenrir might see Wolverine as a rival. He could team up with some dark wizards to try and take down Wolverine and Harry Potter. This would create a complex web of battles and power struggles between different factions in the fanfiction.
In a Harry Potter x Bella Swan fanfiction, the most likely villain could be a combination of characters from both universes. Fenrir Greyback from the Harry Potter world could team up with a rogue vampire from the Twilight world. Greyback's love for chaos and the vampire's thirst for blood could create a really dangerous duo. Another option is Bellatrix Lestrange. She might be jealous of Bella's relationship with Harry (if there is one in the fanfiction) and try to harm her. Plus, her loyalty to Voldemort could make her a major threat as she would carry out his evil plans regarding this new and strange arrival, Bella.
Loki could be an interesting villain in this crossover. Loki, being the trickster god, might see the wizarding world as a new playground for his mischief. He could manipulate some dark wizards into causing chaos, which would draw the attention of both Harry Potter and Nick Fury. Harry, with his knowledge of magic, and Fury, with his strategic mind and resources, would have to work together to outwit Loki and his minions.
Voldemort would still be a very likely villain. He would see the Hulk as a threat or a tool to be used for his own evil purposes. He might try to control the Hulk's mind or use dark magic to make the Hulk do his bidding.
Voldemort could still be the main villain. He might see Noah Puckerman as an oddity in his world and try to use him for some dark purpose or just get rid of him because he doesn't understand where he came from.
It could be an evil Sith Lord who discovers the existence of the Naruto universe and wants to conquer it. He sees Naruto and Ahsoka's alliance as a threat and tries to stop them. This Sith Lord might use his dark side powers to corrupt some of the characters from the Naruto universe and turn them against Naruto and Ahsoka.
It could be Orochimaru. His thirst for power and his willingness to experiment on others would put him at odds with both Naruto and Deadpool. Orochimaru might see Deadpool's regenerative abilities as something to study and Naruto as a threat to his plans. He could try to capture them and use their powers for his own dark purposes.
Maybe a new villain created specifically for the fanfiction. A tech - savvy criminal who wants to steal the secrets of both Stark Industries and Wakanda's technology. This villain could hack into Stark's systems and also try to infiltrate Wakanda. He would be a threat to both Tony and Black Panther as he aims to use their combined knowledge for his own evil purposes.
The Joker could be a great villain. Imagine him getting his hands on some ghostly technology or artifacts from Danny's world. He would use it in his own chaotic and unpredictable way, causing mayhem in Gotham and also attracting Danny's attention. Danny and Batman would have to work together to stop the Joker's mad schemes.