Doctor Octopus is another great option. His mechanical tentacles and his high - level intellect pose a significant threat. You could write a story where he creates a new, more powerful set of tentacles that Spider - Man has to figure out how to defeat.
There could be a genetic engineer gone bad. This villain creates dangerous hybrid creatures and releases them in the city, forcing Spider - Man 2099 to fight these unpredictable beasts. He might also have to figure out how to reverse the genetic mutations.
The Joker would be a great addition. His chaotic nature would contrast well with Spider - Man's quippy and more light - hearted style. Also, Two - Face. His duality could create some interesting moral dilemmas for Spider - Man. And of course, Poison Ivy. Her plant - based powers could make for some unique battles within the asylum's walls.
Spider - Man himself, Peter Parker, is obviously one of the most popular. He is the central character, and fans love to read about his adventures, his struggles with his powers, and his attempts to balance his normal life with his superhero identity.
One great fanfiction idea could be that Gwen discovers Peter's secret identity in a really unexpected way. Maybe she stumbles upon his Spider - Man suit while looking for something in his room. This would create a lot of drama and tension between them as she has to decide what to do with this knowledge.
The Green Goblin is very popular. His chaotic nature and personal vendetta against Spider - Man make for great storytelling in fanfiction.
One interesting story could be about Spider - Man teaming up with a new, unexpected ally. Maybe a villain who has a change of heart and decides to help him fight a greater evil in the fanfiction world. This would add a new dynamic to the usual Spider - Man battles.
One idea could be exploring a different origin story for Spider - Man in the fanfiction. Maybe he gets his powers from a scientific experiment gone wrong in a completely new way. For example, instead of being bitten by a radioactive spider, he could be exposed to a mutagenic serum that gives him spider - like abilities along with some unique side - effects that he has to deal with.
Peter Parker is definitely one of the most popular. After all, he is the main character in the 'Spectacular Spider - Man'. Fans love to see his further adventures, how he deals with new challenges, and his growth as a superhero.
The Vulture could be a likely villain. He might see kidnapping a Spider - Man fan as a way to draw Spider - Man out into the open and then attack him when he's vulnerable trying to rescue the fan. The Vulture could be after some valuable tech that he believes Spider - Man has hidden and thinks the fan might know its location.
There are many great fanfictions out there. One I really liked was where Gwen and Peter went on a road trip together. During the trip, they encountered some small - time villains and had to use their combined wits to stop them without revealing Peter's identity. It was a really fun and light - hearted story.