Perhaps the Ministry of Magic itself could be the main antagonist. They might be corrupt or power - hungry and decide to exile Harry for their own gains. They could be afraid of Harry's influence and popularity among the wizarding community.
It could be a new dark wizard who has risen to power. This wizard might see Harry as a threat to his plans, so he manipulates the situation to get Harry exiled.
A dark force that has the ability to influence the minds of Gryffindor members. This could be a powerful and ancient magic or a new form of dark magic. It turns the house against Harry without them fully realizing it, making the collective Gryffindor house, under this influence, seem like the antagonist.
Perhaps an ancient and dark deity who has been awakened due to some event related to Percy's exile. This deity wants to bring chaos to the world of gods and demigods, and Percy, even in exile, is the only one who can stop it. The deity would use all kinds of dark magic and minions to oppose Percy and his friends.
Maybe a rogue demigod who blames Percy for something and wants to make his exile permanent. This demigod could have some dark powers or be in league with some evil forces. They would constantly try to thwart Percy's attempts to return or find a way to clear his name.
Maybe some sort of combined form of Orochimaru and a powerful Hollow. Orochimaru is always after power and knowledge, and in this fanfiction, he could have somehow made his way into the Bleach world during Naruto's exile. The combined entity would be extremely dangerous, having both Orochimaru's cunning and the Hollow's brute strength.
It could be a power - hungry shinobi from another village. This shinobi sees Naruto's exile as an opportunity to gain more power and influence in the ninja world. He might try to hunt Naruto down to prove his own strength or to steal Naruto's secrets.
Perhaps a long - lost relative of the Potter family who feels they were unjustly excluded from inheriting the manor. This relative could be jealous of Harry's status and the wealth associated with the manor. They might use dark magic to try and claim what they think is rightfully theirs, leading to a battle of magic and loyalty within the Potter family and among Harry's friends.
Voldemort could still be the main antagonist. Even if Demetri has some sort of connection or change in the fanfiction, Voldemort's overarching evil plans would still be a major threat to both Harry and Demetri, especially if Demetri tries to deviate from the Death Eaters' path.
The minotaur itself could be the main antagonist. It's a powerful and dangerous creature, and if it's been set loose in Hogwarts or is guarding something that Harry needs, it would be a major obstacle for him to overcome.
The main antagonist could be a dark wizard who has made the graveyard his lair. He uses the dark energy from the tombstones and the restless spirits there to power his dark magic. Harry stumbles upon this wizard's activities and has to stop him.
A new dark wizard or witch could be the main antagonist. This character, jealous of Harry's fame and power, creates a situation where Harry is framed for a heinous crime. They then ensure his arrest so that they can take over the role of the 'chosen one' in the eyes of the wizarding public and start spreading their own brand of dark magic.