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.
Maybe an interdimensional warlord who sees Goku as a threat to his conquest plans and Lemon as a valuable asset. He would stop at nothing to capture them and gain their powers. He could have an army of minions from different dimensions, making it really challenging for Goku and Lemon to fight back. This antagonist would be very cunning, constantly devising new strategies to outwit our heroes.
Perhaps an ancient evil Saiyan who was banished long ago. This Saiyan would have powers that are unknown to Goku and Vegeta. He could be awakened from a deep slumber and is angry at the current state of the Saiyan race. He sees Goku and Vegeta as traitors for living among the Earthlings and decides to destroy them and take over the universe. His knowledge of ancient Saiyan techniques would give him an edge in battles against Goku and Vegeta.
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.
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.
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.
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.
Maybe a giant lemon - themed monster. This monster is created by some dark force that wants to disrupt the balance between the two worlds in the crossover. It has the ability to spit out acidic lemon juice that can corrode anything. Ichigo has to figure out its weakness and defeat it to restore peace. The monster could be controlled by an unseen force that is the real antagonist behind the scenes.
In a crossover with the Bleach universe, Aizen Sousuke could be a formidable antagonist. His intelligence and powerful abilities would make him a tough enemy for Goku. Aizen could manipulate situations to his advantage, and Goku would have to use his fighting instincts and newfound knowledge of this strange world to defeat him.
Madara Uchiha could still be a great antagonist. Even with Itachi and Naruto teaming up, Madara's power and his long - term plans for the ninja world would pose a huge threat. His knowledge of the Sharingan and his connection to the Uchiha clan would make for an interesting conflict against Itachi, while his overall strength would be a challenge for Naruto as well.