A cool plot could be that an ancient evil force has the power to nullify all Saiyan powers except for Goku and Vegeta's. They are the last hope. However, the evil force has also trapped all their friends and family. So, not only do they have to fight this powerful enemy, but they also have to rescue their loved ones. Along the way, they discover new forms of their Saiyan powers that are not based on anger but on unity and friendship.
One idea could be that Goku and Vegeta are transported to an alternate universe where they have to team up with their alternate selves to defeat a powerful new enemy that is a combination of all the foes they've ever faced. This would force them to not only work together but also understand different versions of themselves.
Maybe there could be a story where Android 18 gets sent to a different dimension and Goku and Vegeta have to follow her to bring her back. In this dimension, the rules of power and fighting are different. They all have to adapt quickly. Goku and Vegeta might learn some new skills from Android 18 as she has a different way of approaching combat situations due to her android nature.
One idea could be a Goku crossover with Superman. They could have an epic battle to test their strength at first, and then realize they have a common enemy and team up. Another idea is a crossover with Naruto. Goku could teach Naruto some of his ki techniques, and in return Naruto could show Goku some of his ninja skills. A third idea is a crossover with Harry Potter. Goku could visit Hogwarts and accidentally cause chaos with his superhuman abilities, but then end up helping the students fight off a dark wizard.
A possible plot could involve an evil force that targets Goku and Female Vegeta specifically because of their combined power. They are constantly on the run and have to rely on each other. In the process, they discover that their ki energies can be combined in a unique way. This discovery not only helps them fight the enemy but also deepens their bond as they realize how well they complement each other.
Maybe in the fanfiction, Goku and Fem Vegeta start a harem as a way to train stronger fighters. They bring in various characters from different planets and train them in their unique ways. Along the way, romantic feelings start to develop between the members of the harem and Goku and Fem Vegeta have to deal with the resulting jealousies and rivalries.
One idea could be that Goku and Vegeta travel back in time to the Saiyan - Planet. They could try to change the fate of the Saiyans, like preventing Frieza from destroying their planet. This would bring a whole new set of challenges as they would have to deal with the Saiyan culture and politics of that time.
For Goku's character development, you can explore his family side more. Maybe he realizes that his constant pursuit of strength is affecting his relationship with his family in the fanfic. Vegeta, on the other hand, could start to open up more about his past traumas. He could learn to let go of his pride a bit when he sees Goku's selfless attitude towards others. This would be a significant development for him.
A possible plot could be that they are transported to a parallel universe where male Saiyans are able to get pregnant. They meet alternate versions of themselves and their friends, and have to adapt to this new world while dealing with their pregnancy. This could lead to many adventures and self - discovery moments for both of them.
Perhaps a fanfiction where Vegeta and Goku get transported to an alternate universe. In this universe, their roles are reversed, and they have to adapt to the new situation while still trying to find a way back home. They would face challenges that are unique to this new world and learn from each other in different ways.
Well, a possible plot could be that Goku and Vegeta are in different high school cliques. Goku is with the friendly and outgoing group, and Vegeta is in the more serious and studious clique. However, a school event forces them to interact. They initially clash due to their different personalities and ways of doing things. But then, they find out they both have a shared goal of protecting the school from a hidden threat. This makes them put aside their differences and combine their powers. Or perhaps they both have a crush on the same girl in high school, and they compete in a friendly way to win her heart, which also leads to some character growth for both of them.