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.
It could still be Voldemort. Even with Revan's training, Voldemort's power and his army of Death Eaters would pose a significant threat. Harry would have to use his newly acquired skills from Revan to finally defeat Voldemort once and for all.
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.
Well, in such a fanfiction, Harry Potter would probably gain some amazing physical abilities from Goku's training. He might be able to move at super - fast speeds and have enhanced strength. His magical skills could also be combined with Goku - like combat techniques, making him an even more formidable wizard in battles against Voldemort or other dark forces.
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.
It could be a deranged fan who has found a way to bring their dark fanfiction ideas to life. This person might be jealous of the original story and wants to create chaos in the wizarding world through their fictional concepts made real.
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.
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.