A frequent theme in 'naruto superhero fanfic' is the idea of Naruto being an outcast even with his new powers. People may be afraid of his newfound abilities or he may feel like he doesn't fit in with the normal ninja community anymore. Also, the theme of using superhero powers to protect the village in a different way than just being a ninja is quite common. For example, he might be able to stop disasters or threats from outside the normal ninja realm. This adds a new dimension to the Naruto universe and makes for some really exciting stories.
Well, the theme of friendship also plays a big role. Just like in the original Naruto story, his friends are there to support him, but now they also have to deal with his superhero side. Sometimes they might be jealous or worried about him. Another common theme is the battle against new and more powerful enemies. These enemies are often too strong for the normal ninja techniques, so Naruto's superhero powers are essential to defeat them. It's all about how Naruto uses his new powers in the context of the relationships and challenges in his world.
One common theme is power - up. Naruto often gets some sort of superhero - like powers in addition to his ninja abilities. Another theme is the struggle between his normal life and his new superhero identity. He has to keep it a secret while still using his powers for good.