One interesting idea could be exploring the psychological impact on the remaining characters. For example, how does Sasuke cope with the sudden loss of so many comrades in a massacre scenario. Another could be the power shift in the ninja world. With many ninjas gone, new alliances might form and old ones might crumble.
Some fanfictions in 'naruto massacre' might focus on the moral dilemmas faced by the characters. For instance, Naruto might struggle with the idea of revenge or forgiveness. Additionally, the rebuilding of the ninja villages after the massacre could be a central theme, with characters having to come together in new ways to restore order and hope.
One interesting idea could be how the themes of sacrifice from Itachi's story in Naruto might be translated into the RWBY universe. For example, Itachi sacrificed his reputation and relationships for the greater good of his village. In RWBY, a character might have to make a similar choice between personal relationships and the safety of the kingdoms. Another aspect could be the combat styles. If Itachi were to exist in the RWBY world, how would his Sharingan abilities blend with the Dust - based combat? It could lead to some really creative fight scenes. Also, the concept of family loyalty, which is strong in Itachi's story, could be explored in relation to the families in RWBY like the Rose or the Schnee families.
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.
One idea could be that Naruto is somehow transported to the world of Athena. He might learn about her powers and the Greek mythology while also sharing his ninja skills. Maybe he could help Athena in a battle against a powerful enemy in her realm using his unique jutsus.