Often, other characters from the Naruto universe also make appearances. For example, the various ninja clans like the Uchiha and the Senju. Their loyalties and relationships with Indra and Asura can add depth to the story. Maybe there are also some original characters created by the fanfiction writer to interact with Indra and Asura and drive the plot forward in unique ways.
A fascinating plotline could be that Indra and Asura are sent on a journey through different dimensions by some ancient jutsu. In these dimensions, they see different versions of themselves and their story. They learn from these experiences and come back to their world with a new perspective, which could potentially change the course of the Naruto universe.
Kaguya could be a great antagonist. Even though she was defeated in the main Naruto story, she could be resurrected or have some lingering influence. Her power - hungry nature and her desire to control everything could put her at odds with Indra and Asura, who are symbols of two different paths in the ninja world. She might try to manipulate them to further her own goals or eliminate them as threats to her reign.
Madara could also be a suitable antagonist. Imagine if he somehow came back to life and found out about Asura and Indra's reincarnation. He would surely try to use them for his own goals, or maybe try to prove that his way of thinking was right all along. He could also use his knowledge of the Sharingan and Rinnegan to create new challenges for Asura and Indra.
Well, perhaps a plot where Asura and Indra are given a chance to rewrite their history. They start to understand each other's viewpoints better and try to create a new future for the ninja world. They could also meet their descendants, like Naruto and Sasuke, in a different dimension and exchange knowledge and power.
One interesting idea could be the exploration of how the reincarnation affects Naruto's relationships. For example, how it changes his bond with Sasuke, as Sasuke is often linked to Indra. Maybe it could lead to a deeper understanding between them, beyond their normal rivalry.
The concept changes the relationships too. Naruto's relationship with Sasuke could be seen in a whole new light. Since Sasuke is related to Indra, they might have a more fated connection. They could be forced to work together more often to fulfill some greater destiny related to their reincarnation status. Also, the way other characters view Naruto could change. They might see him as a more significant figure in the grand scheme of things, not just as a powerful ninja but as a key part of a long - standing cycle.
Obviously, the Indra transmigrant is a main character. Naruto himself might also be involved as he has a connection to the whole Indra - Asura cycle. Sasuke could be another key character as he is also related to this cycle in the Naruto lore.
Often, Naruto himself is a main character in such fanfiction. Since he is the protagonist of the original series and the story might explore how Indra's legacy affects him. Sasuke is also likely to be involved as he has a connection to the Uchiha clan which has ties to Indra. Madara Uchiha could also be a prominent character as he was deeply influenced by the legacy of Indra.
One common theme is the struggle against society. Since their relationship might be seen as unconventional, they often have to face opposition from the world around them.
Naruto and Sasuke are often the main characters focused on since Naruto is the reincarnation of Ashura and Sasuke is the reincarnation of Indra in the Naruto series.