Maybe it's a group of wizards who believe that fanfiction is a threat to the purity of the wizarding world. They create dangerous situations inspired by fanfiction in order to prove their point, and Harry has to fight against them. They see Harry as a symbol of the 'original' wizarding world that they want to change, so he becomes their target.
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.
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.
One possibility is that Harry discovers a world where fanfiction has the power to change the real wizarding world. So he has to train to fight against the alterations caused by these fictional stories. For example, if a fanfiction made Hogwarts a place full of dangerous magical beasts that don't belong there, Harry would need to train to restore order.
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.
It could still be Voldemort. Even though Harry is being trained by Ra's al Ghul, Voldemort remains the main threat in the wizarding world. His dark magic and his army of Death Eaters are still a major problem for Harry and his friends.
There's a chance it could be a powerful house - elf. House - elves are known for their own brand of magic, and one particularly rebellious or enlightened house - elf could decide to train Harry in magic that is more about stealth and quick - thinking. After all, house - elves have to be very sneaky to avoid detection by their masters most of the time, and this kind of skill could be very useful for Harry in his battles against Voldemort.
Maybe it's a former Death Eater who has seen the error of his ways. He wants to atone for his past sins by training Harry to defeat Voldemort. He has inside knowledge of the dark side's tactics and uses this to make Harry a more formidable opponent.
She could be an ancient Celtic goddess, like Brigid. Brigid is associated with magic, healing, and smithcraft in Celtic mythology. In the fanfiction, she might see Harry's potential and decide to train him in her unique magical arts.
It could be a rogue ninja from a forgotten clan. This ninja might have a vendetta against Naruto's village and has powers that are difficult to counter. So, Naruto has to train to kill him to protect everyone.