One interesting plot could be Mario, now as a girl, having to navigate the Mushroom Kingdom in a different way. Maybe she discovers new powers that come with her new form and uses them to save the kingdom from a new threat.
Another possibility is that a group of Koopa minions could be the main antagonists. They might be under the orders of Bowser, but they have their own little schemes going on. They could target Mario - turned - girl because they think she'll be an easier target in her new form, but they are in for a big surprise when she shows her strength.
Well, one possible plot could be that Mario touches a magical item in the Mushroom Kingdom. This item has the power to transform him. As he turns into a girl, he discovers new abilities. Maybe he can now access areas only females can in the kingdom. He also has to deal with how his friends like Luigi react to his new form.
Luigi would probably be very surprised at first. He might be a bit confused, but then he would support his 'sister' Mario. Princess Peach would be delighted. She could finally have a female friend who has all of Mario's skills. Bowser might not even notice at first, thinking it's just another ploy by Mario. But when he realizes it's a real transformation, he might be a bit more hesitant in his attacks, not sure how to deal with this new female Mario.
One possible scenario could be that in this fanfiction, the change forces Kratos to view the world from a different perspective. As a girl, he might face different challenges and reactions from the other characters. Maybe the gods who once feared him now underestimate him, leading to some interesting power dynamics.
Perhaps in a parallel universe, Superman is born as a girl. This version of her grows up with different experiences and challenges. She could be more in tune with female issues in society and use her powers to fight for gender equality as well as the usual superhero stuff like saving the world from villains and disasters.
Another possibility is that Finn - now a girl - discovers new powers or abilities that were hidden before. Since in many stories, a change in gender can sometimes bring out different aspects of a character. She could use these newfound powers to fight against the villains in Ooo in a more creative way than before.
Maybe in this fanfiction, Midoriya as a girl discovers new aspects of her power. Since her body has changed, the way she channels her quirk might also be different. She could then have to train all over again to master this new way of using her ability.
Physically, of course, there would be obvious changes. But personality - wise, he might become more in touch with his emotions. In the original, Lelouch was often very calculating and hid his true feelings. As a girl, society in the story might expect her to be more open about her emotions, which could force her to confront and express them more.
One idea could be that Steven turns into a girl due to a magical mishap. Maybe he was trying to help a gem with a spell and it backfired. As a girl, he could struggle with how others perceive him differently, but also discover new aspects of his personality. He might have to learn new ways to fight and use his powers, adding an interesting twist to the story.