You could also focus on a nukenin's journey to redeem themselves. They might try to make amends for whatever actions led them to be labeled as nukenin. This could involve helping villages secretly or training young shinobi in the outskirts to give them a chance at a better life.
One idea could be exploring the backstories of the nukenin in more detail. Maybe they had noble reasons for leaving their villages that were misinterpreted.
Well, in some 'nukenin naruto fanfic' stories, the missing - nin could form their own small group. This group might not be entirely evil but rather just trying to survive in a world that has shunned them. They could have unique abilities and codes that they follow, which make for an exciting read.
In a fanfiction where Naruto becomes a nukenin, it could be due to a prophecy that the village misinterprets. The village elders think Naruto will bring destruction, so they try to imprison or kill him. Naruto, not wanting to be a victim, escapes and becomes a nukenin. He then travels around, learning new jutsu from other lands and becoming stronger. Eventually, he might come back to the village to show them that their fears were unfounded, but by that time, he has become a very different ninja, with a new set of values and powers.
Perhaps Naruto becomes a nukenin in order to protect a secret that could endanger the village if it were to be exposed. He leaves the village to keep this secret away from those who might misuse it. In his journey as a nukenin, he could develop new jutsu in isolation, away from the constraints of the village's training methods.
One interesting idea could be the combination of Naruto's ninja skills with mecha technology. For example, Naruto might use his chakra to power up the mecha in unique ways. Another idea could be the new enemies that are created specifically for this mecha - Naruto concept, like robotic shinobi that require different combat strategies compared to normal foes. Also, the design of the mecha Naruto itself can be really cool, perhaps with features inspired by the Nine - Tails.
Another idea is that Aizen somehow ends up in the Naruto universe during the time of the Fourth Great Ninja War. He could try to manipulate both sides for his own gain. But Naruto, with his ability to see the good in people, might try to reason with Aizen and show him a different path. It could be a story of redemption or a great battle if Aizen refuses.
In a 'Naruto Mermaid Fanfiction', the mermaids could be in danger from an evil organization that wants to capture them for their precious scales. Naruto teams up with a mermaid princess to stop this threat and in the process, they learn about each other's worlds.
One idea could be a crossover where Naruto and Pucca end up in the same world due to a strange ninja jutsu gone wrong. Naruto is confused by Pucca's constant chasing of Garu, and he tries to help Garu escape in his own Naruto - style way.
Well, you could write a fanfiction where the Nine - Tails in Naruto has some sort of connection to a powerful entity in the Seraphim universe. This connection could lead to a series of events that require Naruto and the Seraphim characters to work together. Or perhaps a character from Seraphim is reincarnated as a ninja in the Naruto world and has to adapt to the new way of life while still having some of their Seraphim abilities.
One idea could be a blacksmith who creates unique ninja tools with special abilities that give the wielder an edge in battle. For example, a kunai that can change its shape during flight to avoid enemy defenses.
You could also write a fanfiction about Naruto being raised by a different clan in the village. For example, if he was raised by the Uchiha clan, it would have a huge impact on his character development and relationships within the village.