How about a villain who has the ability to create illusions? He could make Spider - Man see his worst fears or make the city look like it's in complete chaos when it's really not. Spider - Man would have to rely on his spider - sense to tell the difference between real threats and illusions, and then find a way to defeat this master of deception.
Maybe a villain who can transform into different animals. He could use this power to stalk Spider - Man in the city, changing forms to blend in and then attack when least expected. This would keep Spider - Man on his toes as he tries to figure out the pattern of the villain's attacks and how to counter this shape - shifting ability.
How about a new villain created specifically for the fanfiction? A being made up of the combined negative energy from all the spider - verses. This entity could be called the 'Void - Spider' and it feeds on the chaos and destruction that often follows Spider - Man in his battles. It would be a very powerful and unique threat that the Spider - Men from different universes would have to face together.
Loki could be a great main villain. He could trick Spider - Man into believing that Thor is a threat to Earth and set them against each other. Then, while they are fighting, Loki could carry out his real plan which might involve stealing a powerful artifact from both Asgard and Earth.
Mysterio could be an interesting main villain. He could use time travel to create elaborate illusions across different time periods. Spider - Man would have to figure out which events are real and which are Mysterio's illusions while also trying to stop him from causing chaos throughout time.
Perhaps a new character, like a genetically - engineered super - soldier gone wrong. This villain could have super strength and agility similar to Spider - Man, but with a more aggressive and unpredictable nature. He might see Spider - Man as a rival and be determined to prove that he is the superior one in the city.
It could be a mad scientist who creates mutated creatures to cause chaos in the city.
It could be Loki. He's always causing trouble for the Avengers. He might see kidnapping a fan as a way to mess with Spider - Man and the Avengers, since he enjoys chaos and manipulation.
The Nullifier. This villain has the power to nullify any superpower within a certain radius. He could be a really tough opponent for Spider Man alone as he can't rely on his super - strength or agility when close to the Nullifier.
Mysterio would be an interesting villain for this fanfiction. He could use the chaos of the Age of Ultron to create illusions that further disrupt the city and make it difficult for Spider - Man to tell what's real and what's not. He might also be able to trick the Avengers into believing false threats, causing internal strife within the team.
It could be a combined form of several of Spider - Man's classic villains. For instance, Doc Ock, Electro, and Sandman fused together by some dark magic. This new super - villain would have the intelligence of Doc Ock, the electrical powers of Electro, and the shape - shifting abilities of Sandman. Spider - Man would have to use all of his skills and perhaps some new ones he gains during the crossover to defeat this powerful adversary.
Miles Morales could be a great addition. He has his own unique set of powers and a different perspective compared to Peter Parker. His inclusion could bring new energy and storylines to the team.