Another possibility is that it could be a group of rogue ninjas. They might be envious of Naruto getting such powerful training from the dragons. They could try to steal Naruto's dragon - related powers or stop him from using them. They would likely use their own ninja skills and teamwork to try and take down Naruto, but Naruto, with his dragon - enhanced abilities, would have to find a way to defeat them.
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.
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.
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 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 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.
Another potential antagonist could be an enemy that Orochimaru and Sakura face together during her training. This enemy might have a vendetta against Orochimaru and see Sakura as an extension of him. So while Orochimaru is training Sakura, this new enemy could be the one causing the most immediate problems and danger for them both.
In such a fanfiction, perhaps Naruto could learn unique skills from the dragons. For example, he might gain the ability to breathe fire or fly, which would give him a huge advantage in battles against his foes in the Naruto universe.
It could be someone who wants to steal the knowledge Naruto gained from the Black Panther. Maybe a rogue ninja or a power - hungry villain from another land.
A powerful dark dragon could be the main antagonist. This dragon might be jealous of the little flame dragon's unique abilities or position within the dragon community. It could constantly try to undermine the little flame dragon and cause trouble for it.
Perhaps some of the pure - blood wizard families who look down on house elves training a wizard like Harry could be antagonists. They might see it as a threat to the traditional wizarding hierarchy and try to stop Harry and the house elves, thinking that it's not proper for a wizard of Harry's status to be trained by 'mere' house elves.
Voldemort would still be a likely main antagonist. After all, he is the big baddie in the Harry Potter series. Even with Mace Windu's training, Harry would still have to face Voldemort. However, there could also be new threats emerging from the combination of the Star Wars and Harry Potter universes. Maybe some Sith - like characters could be drawn to the power that Harry is developing under Mace Windu's tutelage.