A powerful and corrupt daimyo could be the main antagonist. He rules with an iron fist, taxing the peasants heavily and suppressing any form of dissent. He sees Naruto as a threat to his power, especially when Naruto starts to gain a following among the oppressed people. He uses his samurai army to try and stop Naruto from spreading the ideas of freedom and equality.
It could be a possessed samurai. This samurai was once a great hero but has been corrupted by an ancient evil spirit. He now goes around terrorizing villages, killing innocent people. Naruto, being the hero, has to find a way to exorcise the spirit from the samurai. The possessed samurai is extremely powerful, with skills that are enhanced by the evil spirit, and he is constantly on a rampage, which makes him a very formidable antagonist for Naruto in the feudal Japan setting.
Maybe an evil shinobi clan that has infiltrated the feudal system. They use dark magic and stealth to manipulate events from the shadows. They want to take over the whole of feudal Japan and see Naruto as an obstacle because of his natural leadership and the loyalty he can inspire in others. They start by assassinating key figures who support Naruto and then directly target him with their most powerful and devious assassins.
One possible plot could be Naruto being born into a samurai family in feudal Japan. He discovers he has strange powers that are not in line with the traditional samurai skills. He then has to hide his powers while also trying to use them to protect his village from a mysterious threat that is slowly emerging, like a group of rogue ninjas from a neighboring land.
For a 'Kamen Rider crossover feudal Japan' fanfic, a Kamen Rider would be a must - have main character. In addition, a ronin, a masterless samurai, could be another main character. This ronin could have his own code of honor and be very skilled in combat. He and the Kamen Rider might meet in a dangerous situation, like being chased by bandits. And there could also be a young princess who is caught in the middle of a political intrigue in the feudal court. The Rider and the ronin might end up protecting her and in the process, get involved in the larger events of feudal Japan.
These stories can show the strict social hierarchy. For example, if a story involves a relationship between different classes, it shows how difficult it was to cross those boundaries. It also reflects on the role of gender. Women in feudal Japan had specific roles, and in erotic stories, it can show how they were expected to behave in relationships, whether it was in marriage or in affairs.
One idea could be to explore how Naruto's ninja skills would be used in the complex political landscape of feudal Japan. Maybe he could be a bodyguard for a powerful daimyo and have to navigate court intrigue.
A powerful rogue ninja who has discovered a way to control digital creatures could be the main antagonist. This ninja might see Impmon as a key to unlocking even greater power and would stop at nothing to capture him. He could use his knowledge of ninjutsu and his new - found ability to manipulate digital entities to create chaos in both the ninja world and potentially the digital world if he were to gain access to it through Impmon.
It could be a rogue ninja who has mastered parkour to an extreme level. He uses his skills to steal important ninja artifacts and Naruto has to stop him. This antagonist would be very fast and agile, making it difficult for Naruto to catch him using normal ninja techniques.
Orochimaru could be a great antagonist. He might want to use Shenron's power for his own dark experiments. He could try to steal the dragon balls and manipulate the wishes to gain immortality or create an army of powerful, immortal ninja.
It could be someone from Miku's world who follows her into the Naruto universe and has evil intentions. Maybe a jealous rival who wants to stop Miku from becoming popular in the new world.
It could be a rogue ninja who wants to use the mummy's power for evil. He might have discovered some ancient scrolls that told him about the mummy's potential and is now trying to awaken it fully and control it to take over the ninja world.
It could be Orochimaru. He has always been interested in the power of the dead and bringing back the strong. He might have found a way to reanimate Naruto for his own evil purposes, like using Naruto's power to take over the ninja world.