One common theme could be redemption. Maybe Naruto helps Mikoto with something from her past. Another could be adventure, where they go on quests together. And sometimes, it's about love against all odds, as their relationship might be seen as unconventional in the Naruto universe.
Common themes often include the power of friendship evolving into something more. Since Naruto is known for his ability to befriend people, it could be that his connection with Mikoto starts as a friendship and then blossoms into a deeper relationship. Also, themes of family acceptance might be there, especially considering Mikoto's family situation in the Naruto lore.
Well, in many of these fanfictions, a common theme is the exploration of different timelines. Authors like to play with the idea of what would happen if Naruto was older and met Mikoto in a different context. Another theme is the discovery of new powers or abilities through their relationship. For instance, they might combine their skills in a unique way that helps them face a common enemy. And of course, the theme of love and its various forms, from a slow - burning love to a sudden, passionate connection, is also quite prevalent.