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.
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.
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.
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.
Another option could be a tech - savvy human who has developed a device to control mutants. He believes that mutants are a threat to humanity and wants to subjugate them. He targets Jean Grey first because of her great power. Tony Stark, being a friend of Jean's and a lover of freedom, teams up with her. Stark tries to hack into the control device while Jean Grey uses her powers to resist the control and fight back against the villain.
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.
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.
Circe is another option. She has the power to transform people and cause chaos. In the fanfiction, she could be jealous of Wonder Woman's beauty and power and Percy's connection to the gods. She might try to turn them against each other by using her magic on them or on those around them, causing misunderstandings and battles.
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.
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.