Maybe it's a group of pure - blood supremacists who don't accept Lemon because she has some sort of unique magical trait that they consider abnormal. They try to drive her out of the wizarding world, and Harry has to fight against them to protect his sister.
It could be a dark wizard who is jealous of the Potter family's fame and power. He sees Lemon as an easy target to get to Harry and plans to use her to lure Harry into a trap.
The main antagonist could be an ancient evil spirit that has been awakened by Lemon's new - found and powerful magic. This spirit wants to possess Lemon to gain full access to her powers and use them for its own dark purposes. Harry then has to use all of his skills and knowledge to save his sister from this malevolent entity.
It could be a dark wizard who wants to use Harry's sister for some dark magic purpose. Maybe he believes that her blood or her unique magical essence can be used to open a portal to a world of dark magic or to resurrect an even more powerful dark force. This antagonist would stop at nothing to get his hands on her.
It could be a jealous wizard who feels that Harry and his sister are getting too much attention in the wizarding world. This wizard might try to undermine their achievements and even put them in danger.
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 dark wizard who has somehow managed to control the Xenomorphs and is using them to cause chaos. This wizard would see Harry as a threat to his plans and would constantly send the Xenomorphs after him, creating those 'lemon' - like difficult and dangerous situations for Harry.
One possible plot could be that Lemon discovers she has a special magical ability that is different from Harry's. For example, she might be able to communicate with magical creatures in a unique way. Harry then has to protect her from those who might want to use her ability for bad purposes.
A powerful and greedy Pokémon collector could be the main antagonist. He might try to steal Ash's Pikachu or other strong Pokémon from them. He would constantly be one step ahead, setting up traps and obstacles for Ash and his sister during their travels.
It could be a member of Naruto's family who is fueling the neglect. Maybe an older relative who believes that the sister has more potential or is more worthy of attention and resources. This person could actively try to keep Naruto down.
It could be Frieza. Since Frieza has a history of hating the Saiyans, he might see Goku's sister as a new threat and try to eliminate her.
Perhaps a long - lost relative of the Potter family who feels they were unjustly excluded from inheriting the manor. This relative could be jealous of Harry's status and the wealth associated with the manor. They might use dark magic to try and claim what they think is rightfully theirs, leading to a battle of magic and loyalty within the Potter family and among Harry's friends.
Their parents' old friends could be main characters. They might come to check on Harry and his sister, bringing gifts and stories about their parents. These friends could offer guidance and protection when needed.