One common theme could be the clash of cultures. Naruto's ninja culture and the Pokemon trainer culture are very different. So exploring how characters adapt to this new culture they're exposed to is a theme.
A frequent theme in 'naruto banished pokemon crossover fanfiction' is the exploration of new abilities. Naruto has his ninja techniques, and Pokemon have their unique powers. When combined in a crossover, there could be a theme of how Naruto might learn to use Pokemon powers or how Pokemon might be influenced by Naruto's ninja chakra. The banishment aspect can also lead to themes of isolation and the search for a new place in the world. For instance, if Naruto is banished to the Pokemon world, he has to find his place among trainers, Gym leaders, and other Pokemon - related entities. This often involves him learning about the Pokemon world's rules and values, which can be a central theme in many such fanfictions.
One common theme is redemption. Naruto, being banished, often has to prove himself all over again in the new crossovers, seeking redemption for whatever led to his banishment in the first place.
Another theme is adaptation. He has to adapt to the new rules, cultures, and powers of the crossover world. For example, if it's a crossover with a magic - based world, Naruto has to learn how magic works and how to use it. This theme of adaptation makes for some interesting character development.
Conflict is a very common theme as well. There are often conflicts between Percy and the new characters he meets, either because of misunderstandings or because they have different goals. And there's also the overarching conflict of Percy trying to find a way back home or to reverse his banishment. This conflict drives the plot forward and keeps the story exciting.
I'm not sure of specific 'naruto banished pokemon crossover fanfiction' titles off the top of my head. But you can try searching on fanfiction websites like FanFiction.net or Archive of Our Own. They usually have a wide variety of crossover fanfictions.
One common theme could be redemption. Maybe the banished character has to go through a journey to prove themselves worthy again, especially in the context of their marriage. Another theme might be the struggle against the stigma of being banished while trying to maintain a relationship.
One of the themes that often pops up is the search for identity. Without the framework of Konoha, Naruto has to figure out who he really is. He might question his loyalties, his goals, and his values. Friendship is also a big theme. We might see how his true friends react to his banishment and if new friendships are formed on his journey.
One common theme is Naruto's struggle for acceptance. After being banished, he has to find a new place in the world where he can be himself and grow. Another theme could be revenge. He might seek revenge against those who banished him. And of course, power - building is a major theme. Naruto has to become powerful in his new situation, often in ways different from what he learned in the village.
Another common character might be Superman. If it's a crossover with the DC universe, Superman's sense of justice and his acceptance in his new world (Earth) could contrast with Naruto's banishment. Naruto could learn a lot from Superman about using his powers for good and also about being a symbol of hope, which could inspire him to find his own way to be a positive force even after being banished from his clan.
Adventure is also a common theme. Picture Ranma traveling through the Pokemon regions, facing different Gym Leaders and trainers. He would bring his martial arts expertise into the Pokemon battles, which would be a new and exciting take on the typical Pokemon adventure.
Isolation is often explored. Being banished means being cut off from the community they once knew. Fanfiction might delve into how the ninja copes with this isolation, whether they become bitter or find new ways to connect with others despite the distance.