Maybe Kaguya Otsutsuki. She's one of the most powerful villains in the Naruto universe. Her powers are otherworldly. Goku would need to use all of his Super Saiyan forms to combat her. He'd have to figure out a way to counter her dimension - hopping and powerful chakra attacks.
Another possibility is Orochimaru. He's always after power and could create some new dangerous experiments. If he targeted Naruto, Goku would have to stop him. Goku might not understand Orochimaru's sneaky and underhanded ways at first, but his pure power and determination would still be a threat to Orochimaru.
It could be someone like Madara Uchiha. He's extremely powerful and his goals are often in conflict with Naruto's. Goku would have to face his Sharingan abilities and his vast array of jutsu.
Maybe it would be a combined form of some of Naruto and Goku's most powerful enemies. For example, if Frieza and Orochimaru somehow combined their powers and knowledge. They would be a very tricky opponent for the fused Naruto - Goku as they would know the strengths and weaknesses of both heroes.
There's also the possibility that Orochimaru could be the main antagonist again. He might be intrigued by Naruto's new powers and try to experiment on him. Orochimaru is always after power and knowledge, and Naruto's Saiyan powers would be something he'd be very interested in. He could use his snake - like abilities and various jutsus to try and capture Naruto.
Maybe it's an ancient evil entity that has been awakened by the combined power of Naruto's chakra and Wonder Woman's divine energy. This entity sees them as a threat to its plan of ruling both universes and thus tries to eliminate Wonder Woman first, which is when Naruto steps in to save her.
Maybe an old enemy of Goku's who has somehow managed to return. This enemy has heard about Goku Jr and figures that by attacking him, he can get revenge on Goku. This could be someone like Frieza who has found a new way to be resurrected and is more powerful than ever.
Perhaps it's a group of mercenary ninjas. They've been hired by someone who has a grudge against Zabuza. They see Zabuza as an easy target when he's alone or vulnerable, but Naruto shows up to spoil their plan.
Perhaps a new and original antagonist could be created for this fanfiction. This antagonist could be a rogue ninja who has mastered a forbidden jutsu that allows him to manipulate time as well. He could be the one who sets up the events that lead to Minato's endangerment, and Naruto has to figure out his motives and stop him while also saving Minato.
It could be a rogue ninja who is using the poochyena for some sort of evil experiment. Naruto has to stop this ninja from harming the poochyena.
It could be a rogue ninja from Tobirama's time who has a vendetta against the Senju clan. This ninja might have been waiting for the perfect moment to strike at Tobirama when he is alone or vulnerable. Naruto then has to face this powerful and vengeful enemy to save Tobirama.
The Locust Queen could still be the main antagonist. Goku would see her as a great threat to the people of Sera. His sense of justice would drive him to take her on directly.
Maybe a mad scientist - type character who has created a device that can disrupt the fabric of reality. He wants to use it to reshape the universes to his own liking. Goku and Lemon get in his way because they are trying to protect their respective homes. The scientist is constantly evolving his device and creating new threats for Goku and Lemon to overcome.