Isolation is a very common theme. Since Castiel is abandoned, he often finds himself alone, cut off from his former celestial family. This isolation makes him question his identity and purpose.
One common theme is Castiel's struggle with his angelic nature and his growing humanity. He often has to choose between following angelic orders and doing what he believes is right. Another theme is his loyalty to the Winchesters, especially Dean. His relationship with Dean is a central focus in many fanfics, whether it's a deep friendship or something more. Also, themes of redemption are common, as Castiel has made many mistakes in the series and fanfics often explore his path to redemption.
One common theme is the clash of different worlds. Castiel, from the dark and often gritty world of Supernatural, finds himself in the bright and magical world of MLP. This contrast often leads to themes of adaptation and understanding.
The theme of unrequited love can be common. Maybe Castiel has feelings for someone who doesn't return them. Guilt is also a big one. He might feel guilty for actions he took that had negative consequences. And the idea of being an outcast. Since he's different from both angels and humans in many ways, he often feels like an outcast, which brings about a lot of sadness in fanfictions about him.
Another theme is friendship. His relationships with the other characters from Supernatural and Ghostfacers are often explored. How he bonds with Sam, Dean, or the Ghostfacers crew is a big part of many fanfictions. In some, he might form a really strong friendship with a new character introduced in the fanfic world.
Protection is also a big theme. Castiel might use his 'nest' to protect something or someone he cares about. It could be a hiding place for a character in danger or a place where he guards important items or secrets related to the 'Supernatural' world.
One common theme is the exploration of their deep emotional connection. Since they have a strong bond in the show, fanfictions often delve into how that bond could turn into a romantic relationship. For example, stories might focus on how they deal with their feelings in a world where hunters usually don't have time for love.
One common theme is the relationship between Castiel and Dean, with Misha's character often playing a significant role in their dynamic. Another is Castiel's journey to understand human emotions better, which can be explored in many different ways in fanfiction.
One common theme is loyalty. In many of these fanfictions, Dean and Castiel show unwavering loyalty to each other, whether it's facing the forces of evil in the Supernatural universe or dealing with personal issues. Another theme is sacrifice. They are often willing to sacrifice themselves for the other's well - being.
One common theme is Castiel's struggle with his identity. His angelic nature vs his growing humanity can often be a trigger for panic attacks. For example, in many fics, he might panic when he realizes he's feeling emotions that are more human - like, such as fear or love in a way that angels aren't supposed to.
Often, the theme of sacrifice is present. Maybe one of them has to make a big sacrifice for the other, and the kiss is a moment of intense emotion before or after that. It could also be about them breaking free from some kind of supernatural constraint that has been holding them back from being together, and the kiss is a symbol of their newfound freedom.