A powerful and corrupt politician could be the main antagonist. He might be using his influence to cover up illegal activities, and Edward, as an honest cop, stands in his way. The politician could try to frame Edward or have him removed from the case.
It could be a crime lord. This crime lord has a vast network of illegal operations, from drug dealing to extortion. Edward's investigations start to disrupt the crime lord's business, so he becomes the main threat. He might send his henchmen to intimidate Edward or try to bribe him to stop the investigations.
An internal enemy within the police force, like a senior officer who is part of a corrupt group. This officer wants to keep the status quo of the illegal activities that benefit him and his group. He sees Edward as a threat because of his integrity and determination to clean up the force, and so he tries to undermine Edward at every turn.
It could be a character who is jealous of the relationship between Roy and Edward. Maybe someone who wanted to adopt Edward themselves or has a grudge against Roy for taking Edward in.
It could be one of the traditional Volturi members who oppose Edward's presence. They might see him as an outsider who could disrupt their long - established order. For example, Caius might be against Edward joining as he's often portrayed as more rigid and less accepting of new vampires in the Volturi.
Maybe a witch who has a vendetta against vampires in general. She could use her magic to cause all sorts of trouble for Edward, like casting spells that prevent him from using his vampire abilities or even creating illusions to drive him mad. Since she's a witch, she has different powers compared to a normal vampire hunter, so she'd be a very formidable antagonist. She might also be able to manipulate other humans or vampires to do her bidding in her quest to get rid of Edward.
A new vampire who is jealous of Edward's relationship with Bella could be the antagonist. With Edward having amnesia, this new vampire could try to take advantage of the situation and win Bella over. They could also try to turn Edward into a more 'evil' version of himself while he is vulnerable.
There could be an organization that wants to keep Ki a secret from the world of alchemy. They see Edward's attempts to learn Ki and potentially bridge the gap between the two as a danger. So, the leaders of this organization send their agents to stop Edward, and the most powerful of these agents could be the main antagonist in the fanfiction.
It could be another alchemist who wants to use this new energy for evil purposes. This alchemist might see Edward as a threat to his plans and constantly try to stop him from learning more about the energy.
Perhaps a corrupt law enforcement officer. He might see Edward as a threat to his own illegal activities or simply want to bring down a powerful mob boss. And Edward's possessive nature towards his operations would make him a prime target for this antagonist. This officer could use underhanded tactics to try and break Edward's hold on the mob world.
Perhaps a new alchemist who is jealous of Edward's skills, even in his new form. This antagonist might see Edward as a girl as an easy target to discredit. They could spread rumors about how Edward's transformation has made him less capable in alchemy, when in fact it's just their way of trying to undermine him.
Maybe Voldemort. If the fanfiction combines the Twilight and Harry Potter universes, Voldemort might see Edward as a threat because he is a vampire and could be allied with Harry. So he tries to drive a wedge between them and make Edward leave Harry.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.