The Akatsuki could also be the main antagonists. They are after Jinchuriki, and Naruto and Gaara being together would be a big target for them. They'd likely try all sorts of sneaky tactics to capture them, which would put Naruto and Gaara's friendship and skills to the test.
It could be Orochimaru. He's always been after Naruto for his special powers. He might set a trap for Naruto, but Gaara intervenes and saves him. Orochimaru's motives of immortality and his dark jutsu make him a great antagonist for this kind of story.
It could be Orochimaru. He might manipulate Gaara into kidnapping Sakura. Orochimaru could have his own devious plans for Sakura, like using her medical knowledge for his experiments. So, he uses Gaara's power and his somewhat unstable mental state at times to achieve his goal. Then Sakura and Gaara would have to team up to fight against Orochimaru.
Maybe a rogue ninja from Gaara's world who somehow follows him into the DxD highschool. This ninja could have a vendetta against Gaara and use the chaos of the DxD world to try and take him down. They could also team up with some of the devils who dislike Gaara's presence to create more trouble for him.
Another possibility is that there could be a rogue shinigami who doesn't like the fact that one of their kind is raising a human. This rogue shinigami could try to undermine Harry's growth and even try to harm him or the shinigami who is raising him.
Maybe it's another dragon, a malevolent one, who sees the female dragon's act of raising a human as an abomination. He decides to target Natsu to prove a point or to gain power over the female dragon. The malevolent dragon could try to undermine Natsu at every turn, creating numerous challenges for him.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
A group of rogue ninja who are hunting nekoshou for their special powers could be the main antagonists. They see Naruto's newfound connection with the nekoshou as a threat and try to eliminate him and the nekoshou he is protecting.
It could be a corrupt ninja from within the village who wants Naruto out of the way. Maybe someone jealous of Naruto's popularity and power, so they frame him and get him sent to prison. This antagonist would then try to keep Naruto in prison by any means necessary.
Madara Uchiha could be a great antagonist. His powerful Sharingan abilities and his grand plans for the Naruto world would put him at odds with Supergirl. He might see her as a threat to his control and try to manipulate or defeat her. Another option could be Kaguya Otsutsuki. Her god - like powers and desire to reshape the world would clash with Supergirl's values and her attempts to protect the people of the Naruto universe.
Maybe it's a ninja who has also been affected by Anodite magic but has turned to the dark side. This ninja could be jealous of Naruto's new powers and want to take them for himself. He would use his knowledge of both ninja techniques and Anodite powers to try and defeat Naruto.