One could expect an exciting adventure. Maybe it'll involve Goku's power being used in a unique way to protect the timeline that Supreme Kai of Time oversees. It could also show a different side of their relationship, perhaps a friendship that develops as they face challenges together.
Another storyline could involve Supreme Kai of Time getting into trouble in a different timeline and Goku having to rescue her. Along the way, they discover new forms of power and new allies.
Well, Vegeta would be a likely character. He might be initially suspicious of the female Goku. Maybe he thinks she's a threat or just can't believe there's another Goku - like being. He could be there to add some comical moments as he tries to understand the situation.
In general, it's a bit of a toss-up. The strength of Manga Goku and Anime Goku can vary depending on the specific arcs and battles. Sometimes, it might seem like one is stronger in a particular situation, but that could change in another.
Another possible main character could be the villain that forces the two Gokus to meet. This villain could be a new, super - powerful threat that the two Gokus need to deal with. Their meeting becomes a crucial part of the story to defeat this powerful foe.
One of the characters who could betray Goku is Piccolo. Although they've been allies for a long time, in fanfiction, things can change. Perhaps an ancient evil force takes control of Piccolo's mind and makes him turn on Goku. Or it could be Krillin. He might be influenced by an outside force that convinces him Goku is becoming too dangerous. Also, don't forget about the Kais. If there's some sort of power imbalance or a threat they perceive from Goku, they might betray him to maintain the order of the universe in the fanfiction.
Well, it could be about Goku Jr learning some of Goku's most powerful moves. Maybe Goku teaches him the Kamehameha. They might also go on an adventure together, like fighting a new and powerful enemy that neither could face alone.