One common theme is the transformation of their relationship. It usually starts with Naruto having a more adversarial or at least a complex relationship with the Kyuubi due to its power, but as the female aspect is introduced, it turns into a love story. Another theme is acceptance. Naruto has to accept this new form of the Kyuubi and his feelings for her, and she has to accept his world and the fact that she's now in a different kind of relationship with him.
Power dynamics is also a big theme. The Kyuubi is an extremely powerful being, and when it's a female in a love relationship with Naruto, it's about how they balance that power. For example, Naruto might gain new powers through their connection, or he has to learn to handle her power in a more intimate way. And of course, the theme of love against all odds. Since they are from different 'worlds' in a sense, their love has to overcome many obstacles like the opinions of others in the ninja world.