Another possibility is Pain. His ideology of bringing peace through pain is very different from what Naruto and Itachi might be aiming for. With Naruto getting stronger through Itachi's training, Pain would see him as a major obstacle to his vision of Akatsuki's dominance and his idea of peace through destruction.
It could be Orochimaru. Since he's always after power and Naruto, with Itachi's training, would become a more appealing target. Orochimaru might see Naruto as a threat to his plans of obtaining all the jutsu in the ninja world.
It could be someone from Guts' world who follows him into Naruto's world. Maybe one of the Apostles. They are powerful and evil beings. Their presence in the Naruto world would be a huge threat and could be a great antagonist as they would have powers that are different from what Naruto is used to dealing with.
It could be someone from Ruby's world who doesn't like the idea of her training an outsider like Naruto. Maybe a powerful mage or a warlord who sees Naruto as a threat to their power or the balance of their world.
It could be a powerful dark wizard who wants to control the dragons and sees Naruto as a threat because of his newfound dragon - trained powers.
Itachi himself could be seen as the main antagonist in this scenario. After all, he is the one doing the kidnapping.
It could be a rogue ninja from a forgotten clan. This ninja might have a vendetta against Naruto's village and has powers that are difficult to counter. So, Naruto has to train to kill him to protect everyone.
Another possibility is that an old enemy of the Uzumaki clan resurfaces. They use Itachi's complex relationship with the village and his own motives to manipulate him into kidnapping fem Naruto. So, this old enemy would be the main antagonist as they are the ones driving the overall conflict.
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.
One aspect of the plot could be Naruto's struggle to control the new power. The Godlike Sharingan is a powerful and potentially dangerous ability. Naruto might initially have a hard time adjusting to seeing the world through the Sharingan's perspective. Itachi would then have to guide him through this process. Also, they could face enemies who are after the power of the Godlike Sharingan that Naruto now has, leading to intense battles where Naruto has to use his new skills and the knowledge Itachi has imparted to him.
Well, it could be that Itachi trains Naruto to better control his chakra. Maybe Itachi sees potential in Naruto to bring peace to the ninja world and decides to pass on his unique skills like the Sharingan's insights on combat.
One possible plot could be that Itachi, seeing Naruto's potential and his importance for the future of the Hidden Leaf, decides to secretly train him. Itachi might teach Naruto advanced jutsu, especially those related to chakra control and unique Sharingan - inspired techniques. Naruto, under Itachi's tutelage, would grow not only in power but also in his understanding of the ninja world's complex politics and the Uchiha clan's history.