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 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.
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.
A new character could be the main antagonist. For example, a powerful alien who has heard of Goku Black's reputation and wants to prove himself by defeating the reincarnated warrior. This alien could have unique powers that are a challenge for Goku Black to overcome, like the ability to nullify ki attacks.
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.
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.
It could be someone who wants to use Naruto's new Buu - like powers for their own evil purposes. Maybe an old enemy who realizes that Naruto in this new form is a huge threat to their plans. For instance, Orochimaru might see this as an opportunity to gain even more power and try to control Naruto - as - Buu.
In a 'Harry Potter trained by Goku' fanfiction, the main antagonist could be an evil wizard who has allied himself with dark forces from other dimensions. This wizard could see Harry, with his new skills from Goku's training, as a major threat to his plans of world domination. He might have powers that are a mix of dark magic and some sort of energy manipulation similar to ki. Harry would then have to use his combined magic and Goku - trained skills to take on this powerful and devious enemy.
Another possibility is that in the world where Goku Black comes from, there is an enemy who follows Goku Black to Izuku's world. This enemy could be a powerful Saiyan or a being with a dark ki similar to Goku Black. They might see Izuku as a weakness in Goku Black's plan and try to eliminate him first, making them the main antagonist in the fanfiction.
It could be Orochimaru. He's always after power and seeing Naruto with Son Goku's power would make him a prime target. He might try to extract the power from Naruto for his own evil experiments.