Well, a popular alternative is the idea of time - travel in Naruto fanfiction. Characters might go back in time to change certain events or gain new knowledge. Then there are those that focus on the training of the younger generation. How the new ninjas are taught by the old - timers like Kakashi or Gai can be really engaging. And don't forget about the crossovers. Some fanfictions combine Naruto with other anime or fantasy worlds, which can be a really fun and creative take on the Naruto universe.
One great alternative theme is the exploration of different ninja clans. You can find fanfictions that go deep into the history, abilities, and relationships within clans like the Uchiha or Hyuga. Another is the development of unique jutsu. Writers often create new and exciting ninjutsu for the characters, which can make for very interesting reads. Also, there are fanfictions centered around the post - war rebuilding in the Naruto world, showing how the characters deal with the aftermath of all the destruction.
Some alternative themes include the exploration of the tailed beasts' personalities and backstories more in - depth. There could be fanfictions where the relationship between Naruto and Kurama is further explored in unique ways. Another theme could be the political intrigue within the ninja villages. How the different leaders make decisions, form alliances, and deal with internal and external threats. And there are also fanfictions that focus on the daily lives of the characters outside of their ninja duties, showing a more human side of them.