One challenge could be acceptance. Naruto has always been known as a boy in the village, and suddenly becoming a girl might make some people distrust or be suspicious of him. Another challenge is physical. His fighting style might need to be adjusted as his body is now different. Also, he might face different social expectations that he's not used to.
One interesting concept could be the unique character transformations that might be different from the original Naruto series. For example, a character could be henged into a combination of different ninja clans' traits.
Naruto himself is often involved. Imagine Naruto henged into a powerful ancient sage form that no one has ever seen before. It would create a whole new set of adventures for him.
One idea could be a crossover where Naruto enters the Incredibles' world and teams up with Elastic Girl to fight a new villain. They could combine Naruto's ninja skills and Elastic Girl's stretching abilities to defeat the bad guy.
Maybe it could be a new character created specifically for the fanfic. This new girl could be from a traveling group of merchants who Naruto meets during one of his missions. Their encounter could lead to a relationship and ultimately the pregnancy.
Another character could be Hinata. She might be more shy around girl Naruto at first but then they could develop a strong friendship. And the Akatsuki members could also have different interactions with girl Naruto. For example, Itachi might see her as a different kind of threat or an interesting enigma, which could lead to some intense confrontations or unexpected alliances.
It could be an unknown girl from a random village that Naruto just happens to pass by and save from a natural disaster, like a flood or a landslide. Naruto's quick reflexes and strength would allow him to rescue her.
One common theme is empowerment. Since the main character is a girl in a male - dominated Naruto world, stories often focus on her rising above the challenges and proving herself as a capable ninja. For example, she might break gender barriers in the ninja academies or in combat.
If Naruto becomes a girl, her character development would be quite distinct. She could start to view the world from a more empathetic perspective. Her experiences as a girl could make her more aware of the inequalities in the ninja world, especially those related to gender. This new awareness could fuel her drive to make changes. For instance, she might start campaigns or initiatives to give female ninjas more equal opportunities. She would also have to adapt to a different physicality. As a girl, her body might be different in terms of strength and agility, which would force her to develop new fighting styles and strategies, thus leading to a different kind of character growth.
It changes the story mainly through character relationships. Since Naruto is a girl, her bond with characters like Kakashi might be different. Kakashi might be more protective of her. Also, her relationship with Jiraiya would be altered. Jiraiya might train her in a different way, considering she is a female.