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.
It could be a dark wizard who wants to disrupt the new relationship between the wizarding world and the queen. This wizard might see Harry's position as a threat to his own plans of taking over the Muggle world starting from the monarchy.
The Volturi Queen herself could be the main antagonist. If she views Bella as a threat to her power or the Volturi's way of life, she would be a very powerful foe. She could use her influence over the Volturi guards and her own powers to try and stop Bella.
Perhaps there's a member of the royal court who is secretly envious of Harry's power and tries to undermine him. This person could be plotting against Harry and trying to make the queen believe that he is a danger rather than an asset. They might spread false rumors or create false evidence to get rid of Harry.
A power - hungry merman who wants to rule over all the mer - people. He sees Harry as a threat because Harry has some special powers or a claim to the throne that he doesn't want to share.
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.
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.
It could be a villain from Harry's world who is jealous of his new connection with the Starks. Maybe a dark wizard who wants to steal Stark technology to enhance their own dark magic.
It could be a corrupt prison warden who has a personal vendetta against Harry. This warden might make Harry's life in prison extremely difficult and try to prevent him from ever getting out, even if he's innocent.
It could be a powerful dark wizard or sorcerer who wants to control both Naruto's world and the Spider Queen's domain. This antagonist might be after the unique powers that Naruto and the Spider Queen possess, like Naruto's chakra and the Spider Queen's web - based magic. He could try to manipulate them against each other to achieve his goals.
It could be a powerful demon who wants to control the Succubus Queen and use her powers for evil. Since Naruto is with the Queen, he becomes a target too.