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.
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.
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.
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.
Gohan would also be a good choice. As Goku's son, he has his own unique abilities. In a fanfiction, they could enter a father - son gaming tournament. Gohan's intelligence and strategic thinking could complement Goku's brute strength in the game.
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.
Goku might run into past versions of his friends. He could see a younger Krillin or Bulma and have some really interesting interactions. He could also meet past versions of his enemies and try to change their fates. For instance, he could meet a young Vegeta and try to steer him away from the path of evil. This would be a huge change in the Saiyan's story.