It could be the Akatsuki. Since Naruto is now following a more Sasuke - like path, he might attract their attention more. They might see him as a potential threat or someone they can manipulate, just like they did with Sasuke.
Maybe Naruto starts to understand Sasuke's motives better. He could embrace Sasuke's idea of seeking power for protection, but in a different way. For example, he might focus more on individual strength rather than relying on the village all the time.
Madara could also be the main antagonist in a different - turn 'naruto return to past fanfic'. If Naruto changes things in the past, it might disrupt Madara's original plans. Madara, being a powerful and ambitious character, would not take this lying down. He could become more aggressive in his pursuit of the Eye of the Moon Plan and Naruto would have to face him in a new set of circumstances, making for a very different and exciting story.
Perhaps an old enemy of Itachi's from his past who has also reincarnated or found a way to exist in the modern day. This antagonist would try to use Naruto's kids as a way to get revenge on Itachi, seeing them as a weak point in Itachi's new - found role as a protector.
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.