Power growth is also a major theme. The main character, often Naruto, has to adapt and grow his power in the new Soul Eater world filled with its own threats. And as he does this, he attracts the attention of the female characters, which ties into the harem aspect. It's about becoming stronger while also dealing with relationships.
One common theme is the clash of cultures. Since Naruto and Soul Eater have different settings and power systems, when combined in a harem fanfiction, there's often a focus on how the characters from each universe react to the other's way of life. For example, Naruto's ninja code might be at odds with the Meister - Weapon system in Soul Eater.