Another option could be a corrupted version of Merlin. What if he was turned evil by some dark magic? He would know all the secrets of both the Arthurian and wizarding worlds. He could use this knowledge to create chaos and try to rule over both. Harry and the good knights of Arthur would have to find a way to reverse his corruption.
A dark wizard from the Harry Potter world, who has somehow discovered the secrets of time travel and has gone back to the time of King Arthur to change history for his own evil purposes. He starts to influence events in the Arthurian era, creating a ripple effect that endangers both the past and the future. Harry has to go back in time to stop him and restore the proper timeline.
Maybe it's a rogue group of wizards who fear Harry's power over Dementors. They might think that Harry is going to use the Dementors to take over the wizarding world in an unjust way. So they band together to try and stop Harry before he can fully embrace his role as the King of Dementors.
It could be a powerful dark wizard who wants to control the spiders for his own evil purposes. He might see Harry as a threat to his plans since Harry is the 'King of the Spiders'. This wizard could be using dark spells to manipulate the spiders and turn them against Harry and the wizarding world.
The mummy itself could be the main antagonist. It could be a mummy that was once an evil sorcerer in ancient Egypt, and now that it has been awakened, it wants to spread its dark magic and rule over both the Muggle and wizarding worlds.
Obviously, Slenderman could be the main antagonist. His spooky nature and his ability to cause fear and disappearances would make him a perfect fit for the role. He could be trying to spread his influence over the wizarding world, which would put him in direct conflict with Harry and his friends.
It could be Voldemort still. Imagine Ares coming into the Harry Potter world, and Voldemort seeing this as a threat to his own power. He would try to either eliminate Ares or use him for his own dark purposes. Ares, on the other hand, may not take kindly to Voldemort's evil ways and so they become enemies, with Harry in the middle trying to defeat Voldemort while also keeping Ares in check.
It could be a dark fairy who is jealous of the Fairy King's alliance with the wizarding world. This dark fairy wants to destroy the connection and take over both the fairy realm and the wizarding world.
In this fanfiction, it could be a group of corrupted magical nobles who oppose Harry's rule. They are used to having all the power in the alternate universe and don't want to give it up to an outsider like Harry. They could be plotting all sorts of schemes to undermine Harry, from spreading false rumors to outright attacking him and his supporters.
Maybe a new character that is created specifically for this fanfiction. This character could be jealous of the attention fem Bowser is getting from both the wizarding world and Harry Potter's group. They could start causing trouble and trying to turn everyone against fem Bowser. This new antagonist could also have some connection to Bowser's original world, perhaps an enemy from there who has followed her to the Harry Potter universe.
It could still be Voldemort. Since he is the main villain in the original Harry Potter series, in this fanfiction he would see the Goddess Lemon as a threat to his plans of taking over the wizarding world. He might try to eliminate her before she can fully use her powers to help Harry and the Order of the Phoenix.
It could be a new dark wizard who has somehow tapped into the power of both the wizarding world and the Narnian magic in a negative way. This wizard might want to rule both realms and is using dark magic from both to achieve his goals.