One common theme is changing the past. Since Naruto travels back in time, he often tries to prevent the tragedies that led to the long - standing enmities between the clans. Another theme is the clash of values. Naruto comes from a more modern - minded era in the Naruto world, and when he enters the warring clan era, his ideas about peace, cooperation, and power are very different from those of the people there.
Well, there's 'Time Traveler Naruto: Warring Clans Edition'. In it, Naruto finds himself in the middle of the chaos of the warring clans era. He has to quickly adapt and figure out how to use his powers in a world that is much more brutal and unforgiving than his own time. It's really exciting as he forms alliances with some clans and tries to outwit the more hostile ones.
I recommend 'Warring Clans: A Naruto Tale'. This fanfiction does an amazing job of showing the different fighting styles of each clan. It also has some unique takes on how the relationships between the clans were formed and broken during that time. It's full of action and drama.
The main conflict could be Naruto's struggle to fit into the very different social and cultural norms of the Warring Clan Era. As a time - traveler, she has modern ideas and values that might clash with the more traditional and clan - centric views of that time.
Perhaps Shikamaru finds himself in the middle of a power struggle between two major warring clans. He has to navigate the complex politics, trying not to take sides directly at first but eventually realizing that one side is more just than the other and uses his skills to help them win. He might use his shadow - based jutsu in creative ways on the battlefield to turn the tide of battles.
Well, in this type of fanfic, Fem Naruto might end up changing the history of the ninja world in the Warring Clan Era. She could use her Uzumaki heritage to her advantage. Since the Uzumaki clan was known for their strong life force and sealing techniques, she could teach these skills to other clans in exchange for peace treaties. Also, she might encounter some of the ancestors of her friends in Konoha, and this could create some really interesting character interactions and story arcs as she tries to shape the future (or rather, the past in this case) of the ninja world.
The mystery. In the Warring Clan Era, there are so many secrets about the clans, their jutsus, and their grudges. Fanfictions in this era often explore these unknowns.
The theme of love and sacrifice also pops up. Fem Naruto may fall in love with someone from a different clan, which adds more complexity to the story. And in some cases, she has to make sacrifices for the greater good, like giving up personal relationships or even her own safety to try and bring peace to the warring clans.
In Naruto time - travel yaoi fanfiction involving warring clans, often the plot may revolve around a character from the present or future going back in time. This can create interesting scenarios where they have knowledge of future events and try to change things within the context of the warring clans. For example, a character might use this knowledge to prevent certain battles between clans or to bring about a different kind of peace. The yaoi aspect can add a layer of romantic or emotional relationships between male characters, which can be set against the backdrop of the clan rivalries and time - travel elements.
He could be a peacemaker. Shikamaru, known for his calm and rational thinking, might try to end the clan wars through diplomatic means. He could hold secret meetings with clan leaders, using his intelligence to persuade them to lay down their arms.