It could be the Hidden Leaf Village's elders. If they are shown to be manipulative and using Naruto for their own political gains, and Naruto eventually finds out, they would become the main antagonists. He might see their actions as the root of all his problems and turn his hatred towards them for exploiting him.
Another possibility is that the main antagonist could be some sort of ancient evil that is awakened by the events in the fanfic. Dumbledore might have given Snape to Harry because he sensed this new threat. This ancient evil could have powers that are unknown to the modern wizarding world and it would be up to Harry and Snape to figure out how to defeat it.
Maybe in the fanfic, Naruto discovers that his parents' death was not as straightforward as he thought. If he finds out that some powerful individuals in the village were actually involved in a conspiracy that led to their deaths, this revelation could be the trigger for his descent into hatred. He might then turn against the village and its leadership, using his powerful jutsu not for protection but for vengeance.
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.
A mysterious figure within Konoha who has a hidden agenda. This person doesn't like the idea of Naruto breaking the norms and wearing a dress. They secretly manipulate events to make Naruto's life difficult while he's in the dress. For example, they might arrange for Naruto to be in situations where his dress - wearing causes maximum embarrassment, all in an attempt to make him conform to the traditional ways.
A powerful and corrupt ninja from another village could be the main antagonist. He hears about the unique knives in Naruto's village and decides to steal them to increase his own power and the dominance of his village. He would stop at nothing to get his hands on these knives, even if it means starting a war between the villages.