The Lizard could be turned into a more supernatural villain. Maybe he gets possessed by an ancient spirit that makes him not only stronger but also able to control other reptiles with dark magic. This would pose a huge threat to Spider - Man as he has to deal with the Lizard's new powers on top of his already dangerous physical abilities.
The Vulture could be a new and more menacing villain. Maybe he's using the post - Civil War chaos to his advantage, stealing high - tech equipment that was left unguarded during the Avenger's split. He could be targeting Spider - Man specifically, seeing him as an easy target now that he doesn't have the full support of the Avengers.
In a crossover with the Marvel universe, Thanos could be a formidable villain. His desire to collect the Infinity Stones and his power would pose a huge threat to the Power Rangers SPD. The Rangers would have to team up with the Avengers to stand a chance against him.
A really cool villain for them to face together could be a shape - shifter. This shape - shifter could take on the forms of their loved ones to trick them. But Spider - Man's spider - sense would give him a hint that something is wrong, and Supergirl's X - ray vision could help them figure out the real identity of the shape - shifter. Also, a villain with the power to control the weather on a global scale would be a great challenge. Supergirl could try to counter the extreme weather conditions, while Spider - Man swings around to rescue people in danger.
Well, the Kingpin could be a main villain. He could see Naruto as a threat to his criminal empire in New York. He might hire some ninja mercenaries from the Naruto universe to take him down. And then there's Electro, who could be enhanced by some sort of chakra - based technology. He could use his new powers to cause chaos in the city and target Naruto specifically, thinking that he's the key to getting even more power.
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.
Shang Tsung would be a great villain. He's always after power and could see Raiden as a threat or a means to gain more power. His sorcery could pose a serious challenge to Raiden. Another one could be Shao Kahn. He wants to conquer all realms, and Raiden's realm would be no exception. His brute force and army could make for an epic showdown against Raiden.
The Shriek can be really interesting in fanfiction. Her sonic powers can be explored in unique ways, like how she uses them not just for destruction but also to manipulate situations or people around Spider - Man.
Maleficent could be a great villain in this fanfiction. Her connection to dark magic makes her a natural fit for the setting of the prison of darkness. She could be the one who put Kairi there or be trying to manipulate her for her own evil plans.
The Green Goblin could be a great main villain in a crossover. Imagine if he teams up with Doctor Doom from the Fantastic Four universe. Their combined evil intelligence and power would be a huge threat to Spider - Man and whoever he teams up with in the crossover.
It could be Doctor Doom. He might be seeking to take over multiple universes in a crossover. Spider Man stands in his way, and Doom, with his superior intellect and powerful magic, manages to defeat Spider Man. His death would then be a huge shock to other heroes in the crossover, like the Avengers or the Fantastic Four who then have to avenge him.