Pain would still be a likely candidate. His Rinnegan gives him a powerful and commanding presence. He has the ability to see the big picture and make strategic decisions for the group.
Again, without more details about the Akatsuki Novel, it's difficult to name the main characters. However, it's common in novels that there could be a strong - willed female character in the Akatsuki. And there may be an older, wiser character who serves as a mentor to the others. There could also be a character with a mysterious past that is gradually revealed as the story progresses.
In Akatsuki fanfiction, one of the possible female Uchihas could be an original character created by the author. For example, she might be a long - lost relative of the main Uchiha clan members. She could possess unique Sharingan abilities that set her apart from the male Uchihas in the story.
One of the most popular female characters in Akatsuki in fanfictions is Konan. Her unique paper - based abilities and her complex relationship with Nagato and Yahiko make her a fascinating subject. In many fanfictions, her backstory is explored more deeply, especially her time growing up in the war - torn land of Amegakure. Another popular one could be Karin. Her connection to Sasuke and her own powers as a sensor type ninja give a lot of room for fanfiction writers to create interesting storylines, like her dealing with her feelings for Sasuke while being involved with the Akatsuki.
Pain would be one of the most challenging. His Rinnegan gives him a wide range of powerful abilities like the Six Paths of Pain. Naruto would have to figure out how to counter each of those paths and find a way to reach the real Pain. Itachi is also tough. His Sharingan and genjutsu skills are top - notch. Naruto would need to break free from his genjutsu and then find a way to fight back against his fire - based attacks.
Itachi could be a likely candidate. He has always had a complex relationship with Naruto. He knows Naruto's potential and his importance in Sasuke's life. Itachi might see Naruto as a key to changing the Akatsuki from within. He could approach Naruto with his calm and mysterious demeanor, explaining to him the real goals of the Akatsuki that are hidden beneath their violent exterior.
Itachi and Kisame could be a pair with a close bond. Itachi is a very reserved person, but Kisame seems to respect and understand him to some extent. They often work together on missions, and this could be seen as a form of 'family' bond within the Akatsuki. Another possibility is Deidara and Sasori. Despite their differences in art forms, they seem to have a connection. Deidara looks up to Sasori in some ways, like a younger brother might look up to an older one.
Konan is often very popular. Her paper - like abilities are really cool and in fanfiction, she can be portrayed in many different ways, like a more sympathetic figure who is just caught in a bad situation.
It could be the main protagonist if the story is written in a way that the character manages to control and utilize all the Akatsuki powers effectively. With the combined powers, they would have a vast array of abilities at their disposal, making them extremely formidable.
I think Hidan would be the most difficult. He was always so hot - headed as an adult. As a baby, he would probably be very fussy and hard to calm down. He might throw tantrums all the time and not listen to whoever is taking care of him.