He could die in battle. Maybe a new, extremely powerful villain emerges who has the ability to nullify Goku's powers or is just so strong that Goku's attacks have no effect. After a long and intense fight, Goku is defeated and dies.
Honestly, comparing the strength of anime Goku and manga Goku is tricky. Both versions have their unique strengths and challenges depicted differently, making it hard to make a clear-cut comparison.
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.