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.
If Kaneki turns into a baby in fanfiction, it could be a way to explore his character in a new light. Maybe he retains some of his memories from his previous form, but is unable to communicate them clearly. This could lead to a lot of misunderstandings and new adventures. Also, it could be a chance for the author to develop new relationships for Kaneki, as a baby he would be more vulnerable and dependent on others.
I really like 'Kaneki's Female Companion'. In this fanfic, the female character has a unique backstory that intertwines with Kaneki's. It shows how their relationship develops in the dark and dangerous world of Tokyo Ghoul. The author does a great job of keeping the essence of the original Tokyo Ghoul while adding their own creative twists.
Kaneki and Touka could be in a situation where they have to team up with some former enemies to save the ghoul community from a new threat. This would test their ability to forgive and their leadership skills within the community.
A fanfic could focus on Rize teaching Kaneki how to fully embrace his ghoul side. She could show him how to use his powers more effectively and how to hunt without attracting too much attention. In return, Kaneki could teach Rize about human emotions and values, which she might have lost touch with over the years of being a ghoul. This exchange could lead to a deep bond between them.
I've heard of a fanfic named 'Eyes of the Self'. In this one, the two Kanekis are constantly at odds, yet they also have a deep understanding of each other. It's really well - written, with great descriptions of their internal battles. There's also a fanfic that's more action - oriented called 'Battle of the Kanekis' where they fight against a common enemy while also dealing with their own relationship. And 'The Kaneki Bond' is a heart - warming fanfic that shows the bond between the two Kanekis growing over time.