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.
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.
There could also be a moment of self - discovery for both of them. Goku might see his past self in Kid Goku and realize how far he has come, while Kid Goku could get a glimpse of his future potential through meeting his adult self. They could share stories about their friends and enemies, like how Goku could talk about Vegeta and Frieza to Kid Goku, and Kid Goku could tell Goku about his early battles with the Red Ribbon Army.
There could also be other characters from the Dragon Ball universe making an appearance. For example, Vegeta might show up. He could be curious about Fem Goku and how she compares to Goku in terms of power. Or Bulma could be there, perhaps she's interested in the technology or biology behind Fem Goku's existence.
Perhaps they would team up against a common enemy. In fanfiction, new threats are often created. They could combine their strength and unique techniques to defeat the bad guy.
In some 'Goku meets Goku fanfiction', they could team up against a super powerful enemy that neither could defeat alone. They would combine their signature moves like the Kamehameha for an ultimate attack.
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.
Maybe an old enemy of Goku's who has somehow managed to return. This enemy has heard about Goku Jr and figures that by attacking him, he can get revenge on Goku. This could be someone like Frieza who has found a new way to be resurrected and is more powerful than ever.