Another storyline could be that Chuck is not as all - knowing as he seemed. Fan fictions sometimes explore the idea that there are things beyond his control or knowledge in the Supernatural universe. He then has to rely on Sam and Dean's instincts and skills more than he expected, leading to a more equal partnership in their adventures.
Castiel can also be an interesting character to pair with Chuck. Castiel's loyalty to the Winchesters and his own angelic perspective can create a contrast with Chuck. Their interactions could explore themes of faith and free will, especially considering Chuck's role as the 'creator' of their world.
One popular theme is Chuck's adventures in the spy world with his unique set of skills and the gadgets he uses. Another theme could be his relationships, like his romantic relationship with Sarah and how they overcome various challenges together. Also, the theme of Chuck growing from an ordinary guy to a confident spy is often explored.
In many cases, Chuck does make an appearance at the end. This can add excitement and resolution to the story. However, there are always exceptions, and it's not a guarantee in every fan fiction.
In some Supernatural Chuck fanfictions, Chuck is often portrayed in different lights. For example, there are stories where he tries to rewrite the entire Supernatural story in a more positive way. Some fanfictions explore his relationships with the other characters more deeply. There are also those that put him in situations where he has to learn from the humans he created, which is a really fascinating concept as it flips the traditional creator - creation relationship on its head.
Well, obviously Chuck himself is a very central and interesting character in these fanfictions. His all - knowing nature and his connection to the overarching story of Supernatural make him a key figure. Sam and Dean Winchester also play important roles as they are the main characters of the original series and often interact with Chuck in interesting ways in the fanfictions.
Chuck himself is very interesting to write about. His transformation from a regular guy to a spy is full of potential for different storylines. Sarah is also great. Her mysterious past and her relationship with Chuck can be explored in many ways.
One common theme is redemption. Chuck often has a complex past in the Supernatural series, and in many fanfictions, his relationship with his mate is a part of his journey towards redemption.
There's a fanfiction where Chuck is actually a time - traveling entity in the Supernatural world. This one is really interesting as it plays with the concept of time and how Chuck's actions across different eras affect the present - day storylines of Sam and Dean. It has some really cool plot twists and character developments.