One idea could be a crossover where Naruto characters end up in the world of Nisekoi. For example, Naruto could meet Raku and they team up for some sort of mission in the Nisekoi city. It would be really cool to see Naruto's ninja skills in that setting.
Another plot could involve a time - travel aspect. Raku and Chitoge could be sent back to a time when their families first had the feud. They could try to prevent the feud from starting, which would change the course of their relationship in the present. This would give them a chance to get to know each other without the burden of the arranged marriage plot.
Chitoge could also be a great focus. Her tough - exterior - but - soft - inside personality would be really fun to explore in the Naruto universe. Maybe she could learn some of Naruto's values like never giving up and it could change her perspective on her own relationships.
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.
One idea could be that Krampus is summoned in the Naruto world during a particularly harsh winter. He mistakes the ninja villages for places full of naughty 'children' (in this case, ninjas who have misbehaved according to some warped view). Naruto then has to convince Krampus that the ninjas are actually good at heart and are just trying to protect their homes.