An anti - hero or a morally grey character might be the antagonist. This character could have a different view on relationships and superhero life. He convinces Spider Man that the harem is holding him back from achieving greater things. And Spider Man, being influenced, betrays the harem.
One possible plotline could be that Spider Man, perhaps due to some mind - control or misunderstanding, turns against the members of his harem. Maybe he starts working with a villain who convinces him that his relationships in the harem are a weakness. Another could be that he accidentally reveals secrets of the harem members, which they see as a betrayal.
It could be a jealous rival trainer. This trainer might have always been envious of Ash's popularity and the loyalty of his harem. So, they plot and scheme to turn the harem against Ash by spreading lies and creating discord among them.
It could be a new character, someone who is jealous of Naruto's growing power and popularity among the girls. This person might spread false information to turn everyone against Naruto. Maybe a rogue ninja who has infiltrated the village and has a vendetta against Naruto for some unknown reason.
Gwen Stacy is an obvious choice. In different universes, she has different relationships with Spider - Man. Another could be Mary Jane. She has always been an important part of Spider - Man's life. Black Cat might also be in the harem as she has a complex and flirtatious relationship with Spider - Man in the comics.
The Green Goblin could be a great main antagonist. He has a long - standing feud with Spider - Man. Maybe in this fanfiction, he could be out for a more brutal revenge after a particularly humiliating defeat. He could target Spider - Man's loved ones or try to completely destroy his reputation in the city.
The Green Goblin could be a great main antagonist even in a Spider Man reborn story. Maybe in this version, he has developed a new form of insanity - inducing gas that affects Spider Man's new powers. Another possibility is Doctor Octopus. He could have found a way to merge his mechanical arms with some sort of alien technology, making him far more powerful and a real threat to Spider Man reborn.
It could be a corrupted version of an old ally. For example, a former S.H.I.E.L.D. agent who was exposed to some strange space radiation. This has turned him evil and he now wants to use his knowledge of Earth and his new - found space powers to create chaos. He blames Spider Man for not being able to save him from the radiation and is determined to make Spider Man pay, all while causing destruction across the galaxy.
Perhaps Doctor Octopus. But instead of just having mechanical arms, his mutation gives him the ability to control any metal object in the city. He wants to take over the city using his newfound powers and sees Spider - Man as the only obstacle.
It could be one of the harem members who has a hidden dark side. Maybe she's jealous of Naruto's closeness to others in the harem and decides to turn the rest against him, so she becomes the main antagonist.
Another option for the main antagonist in the fanfiction could be a jealous classmate. This classmate might be envious of Spider Man's popularity and powers. He or she could try to sabotage Spider Man at school, like spreading rumors about him or trying to get him in trouble with the principal. This would make Spider Man's school life even more difficult as he has to deal with both this classmate and any real threats to the city.