It depends on personal preferences. Some people might think Tokyo Ghoul is better for its original story and character development. Others might prefer Tokyo Ghoul:Re for its continuation and new plot twists.
One interesting female Kaneki fanfiction could be one where she forms an unexpected alliance with a group of ghouls from a different territory. In this story, she might use her unique perspective as both human and ghoul to bridge the gap between different ghoul factions. It could explore her internal struggle in a new light as she tries to maintain her humanity while also fitting into the ghoul world.
One possible fanfiction could be where Kaneki, after fully mastering his ghoul powers, becomes a sort of protector in the ghoul world. He could use his strength to keep the balance between humans and ghouls, defying the traditional enmity. He might be able to create new rules that both sides can abide by, making the world a more harmonious place for both species.
In a fanfiction where Kaneki is overpowered, he could have the power to heal the rift between humans and ghouls in a more radical way. He could use his extreme strength to force the humans to accept the existence of ghouls and also make the ghouls understand the importance of not preying on humans. His overpowered abilities would be like a shockwave that shakes the very foundation of the existing relationships and rebuilds them in a more positive way. For instance, he could create a safe zone where both humans and ghouls can live together without fear, and his overpowered presence would ensure that no one breaks the peace.
The biggest distinction is that Tokyo Ghoul:re builds upon the foundation of Tokyo Ghoul and expands the world and lore. The character arcs evolve differently, and there are new challenges and conflicts. Both manga have their unique charm though.
Self - acceptance is a very prevalent theme. The two Kanekis need to come to terms with their own existence and their relationship with each other. Identity crisis is also common. They both represent different aspects of Kaneki's identity and the fanfic often explores how to reconcile these different identities. Additionally, the theme of power and control can be seen, as they may fight over who gets to be in control in certain situations.