A group of boys who have formed a sort of 'clique' could be the antagonists. They exclude the girl from their group and their resources. They think that girls are weak and don't deserve to share in the benefits of the island. The girl has to prove them wrong and break down their prejudice in order to survive and thrive on the island.
Maybe it's an unseen force on the island, like a spirit or a curse. The girl starts to notice strange things happening around her, like objects moving on their own or hearing eerie voices. The others don't believe her at first, but as the situation worsens, they realize that this unseen antagonist is real and they have to work together with the girl to overcome it.
It could be one of the older boys who is power - hungry. He sees the girl as a threat to his leadership and tries to isolate her from the group. He spreads rumors about her and makes it difficult for her to be part of the decision - making process on the island.
One possible plot could be that the girl discovers a hidden part of the island. Maybe she stumbles upon a cave filled with strange markings and ancient artifacts. She then tries to figure out what they mean and how they relate to the island's history. This could lead her on a journey of self - discovery as well as uncovering the secrets of the island.
It could be a powerful rogue ninja who has made Zacks Island his lair. He might be hoarding some valuable resources on the island and sees Naruto as a threat to his plans.
Maybe a mechanical tyrant in a steampunk - inspired setting. This tyrant has created an army of mechanical beasts and is trying to rule the city. Pyro, as a girl with fire powers, is the only one who can melt the metal parts of the beasts and stop the tyrant. The tyrant sees her as a threat to his rule and is constantly trying to eliminate her.
Maybe a malevolent scientist who has a grudge against female heroes. He believes that only men should have such powers and sets out to take the Omnitrix from Ben and use it for his own evil purposes. He underestimates Ben because she is a girl but soon realizes his mistake.
It could also be a new villain that is specifically interested in Sonic because she is now a girl. Maybe a villain who has some sort of vendetta against female heroes or wants to use Sonic's new form for some evil experiment. However, Dr. Eggman is so iconic in the Sonic series that he would be a strong contender for the main antagonist role even in this fanfic scenario.
It could be an evil wizard who was the one who actually caused Gumball to turn into a girl in the first place. The wizard has some ulterior motives, like using Gumball's new form to gain power or to cause chaos in the town. He tries to prevent Gumball from finding a way to turn back and keeps creating obstacles for Gumball and her friends.
It could be a villain who is obsessed with creating chaos through strange transformations. This villain might have targeted Deku specifically because of his status as a rising hero. They want to see how Deku will cope with being turned into a girl and use it to undermine his confidence and hero image.
It could be a character who somehow discovers Izuku's secret and tries to use it against her. Maybe a rival at school who is jealous of Izuku's progress and sees this as a way to get her expelled or discredited in the hero community.
Another possibility is that an alien race that Ben has previously encountered and thought was friendly, now turns against him/her because of the change in gender. They might have some strange beliefs or customs that make them view Ben's new form as a threat or an abomination, and thus they become the main antagonists in the fanfic.
Ganon could still be the main antagonist. Even though Link has turned into a girl, Ganon's goal of taking over Hyrule remains the same. He might underestimate Link in her new form, which could give Link an advantage. For example, Ganon might not expect the girl - Link to be as strong or resourceful as the male Link, but she proves him wrong.