A group of rogue werewolves from Bella's world who have made a pact with a minor demon from the Charmed universe. They could be an antagonist in the fanfiction. The werewolves could use the demon's knowledge of magic to enhance their own abilities and start causing chaos in both worlds. Their goal might be to overthrow the current power structures in both the Twilight and Charmed universes.
A dark warlock from the Charmed universe who has somehow discovered the existence of vampires through Bella could be an antagonist. He might see the vampires as a new source of power and try to use Bella to gain access to the vampire world. He could also be interested in Chris's powers and try to steal them to increase his own magical might.
A powerful vampire - witch hybrid could be a great antagonist. This character could combine the strength and immortality of a vampire with the magical abilities of a witch. They might envy Bella's connection to both the vampire and human worlds, and also be jealous of Chris's powerful magic lineage. Their goal could be to create a world where vampires and witches rule over humans.
One idea could be that Bella, with her experience in the supernatural world from the Twilight series, somehow crosses paths with Chris Halliwell from Charmed. They could team up to fight a new kind of evil that combines the dark magic from the Charmed universe and the vampire - werewolf related threats from Bella's world. For example, a coven of vampires who have learned some dark spells.
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.
Another possible antagonist could be a rogue ninja from Hailbel's past. This ninja could have a vendetta against her family or something she did in the past. When he discovers that Hailbel is with Naruto, he decides to take them both on. He might have some unique and dangerous techniques that Naruto and Hailbel have to figure out how to counter.
It could be a dark wizard. Dark wizards are often associated with using dark arrows as weapons in fanfiction. They might have a vendetta against Chris for some reason, like he unknowingly disrupted one of their dark magic experiments.
Alice Cullen can be a very popular character. Since she can see the future, in a 'reborn as bella swan' scenario, her interactions with Bella could be really different. Maybe she tries to guide Bella in a new way based on her visions. Also, Carlisle Cullen is popular. His father - figure role towards Bella might be explored further in these fanfictions.
Another possible antagonist could be the CCG in the 'Tokyo Ghoul' universe. If they were to somehow cross paths with the 'Death Note' world, they might see the power of the Death Note as a threat and try to take it. This would put them in direct conflict with both Kaneki and Light, as Light wouldn't want to lose his tool for 'justice' and Kaneki wouldn't want the CCG to gain more power to hunt ghouls. So, in this complex crossover situation, the CCG could end up being an antagonist.
It could be a jealous vampire who doesn't like Bella's new - found power. Maybe this vampire wants to be the most powerful being in the area and sees Bella as a threat.
A powerful werewolf could be the main antagonist. In the fanfiction world, werewolves and vampires often have a tense relationship. If Bella's sister does something that angers the werewolves, like stealing from their territory or harming one of them accidentally while doing her criminal deeds, the werewolf pack leader could become the main antagonist, vowing revenge on the sister and by extension, Bella and the Cullens.
Vlad Masters could be a likely antagonist. He might see Kim as a threat to his plans regarding Danny. Since he's always looking for ways to get Danny on his side or out of the way, he could try to use Kim as a pawn. Maybe he tries to manipulate Kim into thinking Danny is the bad guy, or he uses his ghost powers and wealth to create problems for both of them.
Perhaps an ancient evil entity that was once sealed away but is now breaking free. It wants to destroy all the good in both of their worlds, and Feyre and Aelin are the only ones who can stop it. The entity would be extremely powerful, with abilities that can counter both Feyre's and Aelin's powers to some extent.