It really depends on the writer's preference. Some fanfictions might have Naruto winning because of his unwavering belief in friendship and his ability to draw on the power of the nine - tails. Others might have Sasuke winning due to his strategic mind and mastery of the sharingan.
Naruto would likely win. Godlike Naruto implies he has extraordinary powers. Naruto has strong chakra reserves, and his signature jutsus like Rasengan are extremely powerful. Also, his ability to quickly adapt in battle gives him an edge over Orochimaru.
In other fanfics, Jason comes out on top. His leadership skills and ability to control the wind and lightning can give him an edge, especially when the battle takes place in an open area. Also, his Roman military training sometimes gives him an upper hand in strategic battles.
Wonder Woman usually wins in their encounters. She has a wide range of abilities. Her bracelets can deflect attacks, and she can fly, which gives her mobility that Poison Ivy lacks. Poison Ivy is mainly focused on her plant powers. Although she can create large and dangerous plants, Wonder Woman can use her indomitable will and fighting skills to break through Ivy's defenses. Also, Wonder Woman's experience in dealing with various threats in the DC universe gives her the knowledge and strategy to take on Poison Ivy effectively.
Kabuto is also common. He was Orochimaru's right - hand man. In fanfiction, he could be used to either further Orochimaru's plans against Naruto or he could have a change of heart and help Naruto against Orochimaru. His medical skills and knowledge of Orochimaru's secrets make him an interesting addition to the story.
He could have the power to instantly heal any injury. His chakra might be so vast that he can create multiple clones without getting tired. Also, he might be able to control the elements in ways that are beyond normal shinobi capabilities.
Danzo could be a main antagonist. He might see Orochimaru's interest in Naruto as a threat to his own plans for Konoha. He could try to eliminate Naruto or use him as a pawn against Orochimaru, all while hiding his true intentions from the rest of the village.
No. It's not fair. Fiction should be more inclusive and diverse. Just because of the traditional view that men are stronger doesn't mean female characters should always lose in fights. It limits the potential of female characters.