It could be a new dark wizard that is specifically drawn to Harry because of his different Patronus. This wizard might see Harry's unique Patronus as a threat to his own plans for power or chaos in the magical world.
There could be an ancient magical creature that has been awakened by Harry's different Patronus. This creature, with its own motives and powers, might oppose Harry because his Patronus represents a change in the magical balance that it doesn't want to accept, thus becoming the main antagonist.
Another possibility is that an old rival of Ash's, who has always been jealous of his success, becomes the main antagonist in this fanfiction. When Ash chooses a different starter, this rival sees it as an opportunity to finally defeat him, thinking that Ash's new and untested starter will be his downfall.
Perhaps it would be a new character entirely. A powerful wizard who is jealous of Harry's arrival in this new world and sees him as a threat to his own power and status. This wizard could have control over a group of magical beings that are unique to this world and use them to oppose Harry at every turn.
If Harry decides not to go to Hogwarts, the main antagonist could be the Ministry of Magic. They might see Harry as a threat since he's trying to practice magic on his own without proper supervision. They could send Aurors after him to stop him from causing any chaos in the Muggle world or from becoming a powerful, unregulated wizard.
It could be a dark wizard who has a vendetta against the Weasley family. Since the twins are part of the Weasleys, this dark wizard targets them. Maybe he blames the Weasleys for something that happened in the past, and the twins, being the more adventurous and visible members of the family, become the main targets.
Well, perhaps in this fanfiction, Harry's different Patronus could be something unexpected like a phoenix. It might signify a new aspect of his character, such as a stronger connection to the magical world's renewal and rebirth. Maybe this different Patronus is a result of an alternate event in his life, like a different encounter with a powerful magical being that changed the form his Patronus takes.
A new dark wizard could be the main antagonist. Maybe someone who was inspired by Voldemort's ideology but has new and more devious ways of causing chaos in the wizarding world. This antagonist could target Harry Potter's son to prove himself as a more powerful and feared dark wizard.
A pegasus Patronus is also a great concept in fanfiction. Pegasus represents grace and freedom. A character with a pegasus Patronus might be someone who values these qualities. They could be the type of person who is always looking for a way to break free from constraints, whether it's social norms or dark magic threats in the wizarding world. This Patronus could also suggest a connection to the skies and a more spiritual side of magic.
A new dark wizard who has emerged from the shadows, someone who idolized Voldemort and is trying to pick up where he left off. This antagonist could be using new and more insidious magic that Harry has to figure out how to combat as an Auror.
A power - hungry noble could be the main antagonist. This person might be jealous of the Queen's position and wants to overthrow her, and sees Harry as an obstacle in his way.
Perhaps Voldemort himself, even though he doesn't have the natural ability to shapeshift in the original story. In the fanfiction, he could find a way to mimic shapeshifting, or he could use dark magic to control other shapeshifters to go against Harry. This would make for an even more dangerous and complex conflict as Harry has to face his greatest enemy with this new aspect of his powers.