Well, obviously Jak and Kyrie are the main characters. Jak is often depicted as a brave and strong hero with his own set of skills and abilities. He has a complex past which can be explored in the fanfiction.
Perhaps Jak has to prove himself worthy to Kyrie's family in order to be with her. This could involve him taking on difficult quests and showing his loyalty and courage. Meanwhile, Daxter could be there as a comical sidekick, adding some humor to the story.
The Jak and Daxter story does have an end. However, fans often imagine what could happen next or create their own continuation scenarios in their minds.
One great 'jak and daxter fanfiction' I read was about Jak's origin in more detail. It really explored his past before the events of the game and added a lot of depth to his character.
The Precursors are very important in the Jak and Daxter universe, and including them in a crossover fanfiction could add a whole new level of depth. They could be the key to understanding the new world they cross into, or perhaps they have a hidden agenda that Jak and Daxter have to figure out. Also, the Metal Heads could be included in a more action - packed crossover, where they pose a threat not only in their own world but also in the crossed - over world.
In Jak and Daxter fanfiction, a normal human could also be a source of help. Maybe they provide shelter or food to Jak and Daxter during their travels. They could be the ones who give important information about the secrets of the land, like the location of a hidden Precursor artifact or a dangerous enemy's lair. Since they are normal humans, they might not have the special abilities of Jak and Daxter, but their local knowledge can be invaluable.
There might be a fanfiction where Daxter gains the ability to use chakra. He tries to learn ninjutsu from Naruto. It would be a humorous story as Daxter is a small ottsel and his attempts at using powerful ninja techniques could lead to all sorts of comical situations. Like when he tries to do a Rasengan and just ends up spinning in circles.
Naruto and Jak make a great pair. Naruto's optimism and determination combined with Jak's more brooding and powerful nature can create a great dynamic. They can learn from each other's strengths and weaknesses.
One great 'jak and daxter x reader fanfic' is 'Jak's Adventure with You' which has an exciting plot where the reader character joins Jak on his quests. It really makes you feel like you're part of the Jak and Daxter world.