Obviously, the first male ninja would be the main character. But there could also be his mentor, someone who guides him in his ninja training. Maybe an old and wise ninja who has a lot of knowledge about different jutsus.
One possible main antagonist could be an ancient evil ninja who was sealed away long ago and is now awakened by Naruto's new - found power. This antagonist might see Naruto as a threat to his plans of world domination and tries to stop him at every turn.
Naruto himself is likely to be a main character. Since it's related to Naruto, he'll probably be at the center of the story, with his journey to become Hokage or his relationships with other characters like Sasuke and Sakura being explored further.
The plot could center around the first male ninja facing some great threat to the ninja world. He might be on a quest to find a powerful jutsu or artifact to save everyone. Along the way, he could encounter various challenges, make new friends and enemies, and his character could develop as he overcomes these difficulties. For example, he could start as a novice and gradually become a respected and powerful ninja.
In this fanfiction, Naruto could be given god - like speed, strength, and intelligence. Since he is the first male ninja with these powers, he decides to rewrite the rules of ninjutsu. He might start training other ninjas in a new way that focuses on inner power rather than just physical techniques. This could lead to a revolution in the ninja world where Naruto is seen as a pioneer and a hero.
It could be Orochimaru. He's always been after power and new jutsu. If Naruto is guarding something really valuable, like a new powerful ninja technique, Orochimaru would be a likely antagonist. He'd stop at nothing to get his hands on it.
It could be Danzo. He was always a bit of a shadowy figure in the Naruto series. In a ninja tribunal fanfiction, he could be working behind the scenes to manipulate the tribunal for his own gains, perhaps trying to get rid of those who oppose his more extreme views on protecting the village.
It could be Orochimaru. He is always after power and Naruto's new silent and perhaps more powerful form could be a threat to his plans, so he would try to stop Naruto.
The main character is clearly fem Naruto. But depending on the plot, characters like Kakashi could also be important. He was Naruto's teacher and could play a role in guiding fem Naruto in using her seduction skills in a proper and strategic way. Also, villains from the Naruto universe might be main characters too, as they would be the ones that fem Naruto would be using her seduction skills against.
Often, there could be an unnamed or newly created ninja who is the main character. This ninja has lost everything and is now homeless. He or she is usually on a quest to regain their former status or find a new purpose in life.
It could entail the first male ninja's struggle to gain acceptance in a world that might be dominated by different power structures initially. Maybe he was from a small village and had to prove himself against bigger, more established ninja groups.