Survival is a very common theme. Characters are often in situations where they need to find or maintain shelter to stay alive, whether it's from a physical threat like a storm or a more complex danger like a war. Another theme is community. Since shelters usually involve groups of people, how they interact, cooperate or compete within the shelter environment is often explored.
One common theme is adventure. Writers often take the characters from Shelter and Rin and put them in new and exciting situations. For example, they might go on a quest in a fantasy world.
One common theme is neglect. For example, shelters might not have proper medical facilities or staff to take care of the sick and injured. So, people with health problems just suffer without proper treatment.
Abandonment is a very common theme. Like dogs being left behind when their families move or get a new pet. Another theme is neglect. Some dogs come in with poor health due to being ignored by their previous owners.
One common theme is the clash of cultures. Since Naruto has its own distinct ninja culture and Cait Shelter has something different, fanfictions often explore how these two cultures interact. For example, how the values of friendship and loyalty in Naruto compare to those in Cait Shelter.
One of the main themes is friendship. Just like in the original My Little Pony series, ponies in Shelter MLP fanfic often rely on their friends and form strong bonds. Another theme is discovery. Since it's set in a Shelter, there are often elements of ponies discovering new things about the Shelter itself or about each other. Also, the theme of community is prominent. Ponies work together to build and maintain their Shelter community.
Love and bonding are also prevalent themes. The love between the caregiver and the child develops over time. In 'Yotsuba&!', we can see the strong bond between Yotsuba and her father. Additionally, the theme of learning is there. The caregiver often has to learn about childcare, like how to cook for the child, how to handle their emotions, etc.
A common theme is the battle against the unknown. Exterminators often face strange and dangerous creatures, so there's a lot of mystery and exploration involved.
In omegaverse light novels, a frequent theme is the concept of marking. This is a way for alphas to claim omegas and is a very important part of the relationship. Another common theme is the idea of scent. Scent plays a crucial role in attraction and identification in the omegaverse. Also, the theme of survival in a world where the biological differences can sometimes put characters in difficult or dangerous situations is often explored.
Another theme is power and its corruption. Many undead characters gain great power, and this power can either be used for good or lead them to be corrupted. For example, an undead sorcerer might start off with good intentions but as he gets more powerful, be tempted by darker forces.
Romance is a huge theme. The attraction between alphas and omegas is a central focus. It can be a sweet and passionate love, or sometimes a more complex and angsty relationship, especially when dealing with the social norms of the omegaverse society which might not always be accepting of certain pairings.