One possible fanfic could be about Goku's intense training before the Cell Games. He might be shown pushing his limits in the Hyperbolic Time Chamber, trying out new techniques and forms to defeat Cell. Maybe he discovers a new power level that no one, including himself, expected.
First, give the MC a clear backstory. For example, if they are a human, explain where they come from, their family, and what led them to get involved with the events related to Cell. Maybe they were training in martial arts because they had a personal vendetta against powerful beings after their family was killed by a random villain. This would give them a motivation to face Cell.
If Goku and Female Cell interacted, it could change the perception of enemies in the DBZ universe. Their cooperation might lead other fighters to be more open to the idea of redeeming former foes. For example, if they manage to work together successfully, Vegeta might rethink his stance on some of the villains he's faced.
The theme of transformation is also popular. It could be a physical transformation of the female Cell, or a more emotional and mental one as she navigates the complex world of DBZ, often changing from a more villainous or neutral stance to a more heroic one.
One interesting fanfiction could be where Cell somehow ends up in the Naruto universe. Maybe he's a new type of enemy that the ninja have to face. It could bring a whole new level of danger as his powers are different from the normal jutsu - based attacks in Naruto.
It's hard to say for sure. Different people might have different ideas of how the story ideally should have ended depending on their expectations and interpretations.
It depends on the genre and the themes of the story. Different types of stories might have very different ideal endings based on what the readers or viewers expect and what the story has built up to.
One idea could be to explore what if Gohan had a different training partner before the Cell Games. For example, if Piccolo had trained with him more intensively, it might have changed his power level and fighting style during the games.