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.
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.
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.
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 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 or witch could be introduced as the antagonist. This character could be even more powerful and cruel than Voldemort. They could have a special power that allows them to break Harry's spirit, perhaps by constantly torturing his mind or by causing harm to those he loves in ways that are even more insidious than Voldemort's methods.
Perhaps a long - lost relative of Voldemort who has been in hiding all these years. This relative has discovered a way to gain power through Harry's kid. They might start by infiltrating Hogwarts under a false identity and slowly manipulate events to get closer to the kid. Their ultimate goal could be to sacrifice the kid in a dark ritual to bring back the dark days of Voldemort's reign.
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.
It could be a rogue wizard who has also acquired Muggle weapons and is using them to cause chaos. This wizard might be jealous of Harry's fame and wants to use the gun to prove that he's more powerful.