The Kingpin could be a great antagonist. He could be trying to take over more of the city and sees Spiderman and Tigra as threats to his plans. He uses his criminal network and his physical strength to try and stop them.
The symbiote could be the main antagonist. It could be a new and more powerful version that can infect mutants as well as non - mutants. It targets Female Wolverine first, trying to use her mutant healing factor to enhance itself further. Spider - Man gets involved when he realizes the symbiote is causing chaos in the city. The symbiote's ability to take over its host and gain their powers would pose a significant challenge for our heroes.
The Green Goblin could be a great main antagonist. He could be jealous of the new team - up between Spiderman and Agent Venom and see them as a threat to his own plans for the city. So he devises a series of traps and attacks to try and take them down.
The Green Goblin could also fit well. He could form an alliance with some of Wonder Woman's foes. His chaotic nature and love for destruction would contrast with the heroes' quest for peace. He could target both of them, trying to break their partnership and cause mayhem in the city.
Green Goblin could also work well. He could be jealous of all the attention Spiderman is getting at the homecoming and decides to crash the party. His maniacal nature would contrast well with Deadpool's zany humor and Spiderman's more responsible heroism.
A combination of Green Goblin and a chaos - causing creature from Equestria. The Green Goblin could team up with this creature and use his glider and bombs along with the creature's ability to spread chaos. They would target both Spider - Man's city and Twilight Sparkle's home, causing destruction and trying to assert their control.
It could be Doctor Octopus. He might team up with some evil spy organization. His mechanical arms and scientific knowledge combined with the sneaky tactics of the spies would make for a formidable foe for Spiderman and the Totally Spies.
Venom could also be a main antagonist. Imagine if he somehow got enhanced and became even more powerful. He could be causing chaos in the city, and both Spiderman and Deadpool would have to figure out a way to defeat him. Deadpool's lack of fear and Spiderman's knowledge of Venom could be key factors in their fight.
Venom could be a main antagonist in this crossover. If Venom were to find his way to Gotham, he would be a formidable foe. His strength and aggression combined with his alien symbiote abilities would make him a tough opponent. Batman would have to rely on his gadgets and strategic thinking, while Spiderman, having prior experience with Venom, would have to use his knowledge of the symbiote to try and stop it. And Venom's desire to spread chaos and destruction would put both heroes in a difficult situation.
It could be someone like Doctor Octopus who gets his hands on some ninja technology. He could use it to enhance his mechanical arms and also start stealing chakra from people to power his new devices. His scientific mind combined with the newfound ninja powers would make him a formidable foe for Naruto and Spiderman.
The Joker could be a great main antagonist. Imagine he teams up with some of Spider - Man's foes like the Green Goblin. They could create a chaotic plan to take over both Gotham and New York. Their combined madness would be a huge threat to both Batman and Spider - Man.