The fanfiction might focus on how Fem Naruto imparts her ninja skills and values to her son. For example, she could teach him the importance of perseverance and loyalty, just as Naruto learned from his own mentors. The son could also inherit some of Naruto's special abilities, but in a different way due to being a different gender from the original Naruto.
The son's character could be developed through his interactions with his mother. He might be inspired by Fem Naruto's courage and determination, and grow up to be a strong - willed ninja. For instance, seeing his mother face difficult situations could make him want to be just as brave.
Another possibility is that it's a result of some strange chakra experiment gone wrong (or right). Scientists in the Naruto universe are always dabbling in chakra research. Maybe an experiment meant to enhance her natural abilities instead gives her the Rinnegan, and she then has to learn to control it quickly to avoid being consumed by its power.
One possible plot could be that Naruto grows up with a unique connection to the fem Kyuubi. Since his mother Kushina was also linked to the Kyuubi, Naruto might have an even stronger bond. He could learn special jutsus from the fem Kyuubi's chakra, which makes him stand out among his peers in the ninja academy. His relationship with the fem Kyuubi could be like a mentorship, guiding him on his path to become a great ninja.
His powers would likely include some form of soul manipulation. He might be able to sense the souls of others more acutely, which could give him an edge in battle by predicting his opponents' moves.
His development could be quite different. Since he has this special connection to the fem Kyuubi and is Kushina's son, he might grow up with a more refined sense of chakra control. This would make his training easier and he could progress faster in his ninja skills. Also, his attitude towards his enemies might be more understanding, as the fem Kyuubi could have taught him about the reasons behind people's actions. He could become a more diplomatic ninja, trying to find peaceful solutions first instead of just jumping into battle.
Naruto would likely be more in tune with his emotions. Since the Fem Kyuubi could potentially have a more nurturing influence, he might not be as brash and loud as in the original story. He could be more introspective and have a deeper understanding of the power he holds from a young age. This would change his interactions with his peers, as he would seem more mature in some ways.
One idea could be that the daughter has to hide her identity in the village that banished Naruto. She might inherit some of Naruto's unique abilities like his shadow clones. She could use these abilities in secret to help the villagers without them knowing she's related to the banished Naruto.
One possible plot twist could be that Naruto has the ability to control the souls of the dead, inherited from his mother, the Fem Shinigami. This could lead to him being able to communicate with past Hokages in a more direct way than just through their chakra imprints. Another plot twist might be that Naruto has to face an enemy who is also related to the Shinigami realm and his connection to it is the key to victory.
Perhaps a plot twist could be that the village initially rejects Naruto due to his relation to Fem Madara. They fear he might turn out like his mother and bring destruction. This would force Naruto to prove himself in a different way than in the original series. He might have to find allies outside the village and then come back to redeem himself in the eyes of the villagers.