DIO could be a likely villain. Since he has a long - standing feud with the Joestar family. He might try to take advantage of the situation where Jotaro and Jonathan meet to cause chaos and try to defeat them both.
In this fanfiction, perhaps they could have an epic battle against a common enemy. Jotaro with his Star Platinum and Jonathan with his Hamon could combine their powers in a unique way.
One likely villain could be Loki. He's always up to no good and loves to play mind games, so a card game would be right up his alley. He might be the one who lures Tony into the game.
The Joker could still be a major villain. Even with Batman as a god, the Joker might find some twisted way to challenge him. Maybe he'd try to drive Batman to use his god - like powers in a way that goes against his moral code. Ra's al Ghul could also be a villain. He might see Batman's new godhood as a perversion of the natural order and seek to destroy him.
The gorgons could be a likely villain. They might be lurking in the catacombs of Paris, waiting to turn Percy and Annabeth into stone. They could be after some powerful magic item that is hidden in the city.
It could be Danzo. He's always been a shadowy figure with his own agenda in the Naruto series. In a massacre fanfiction, he might be behind it all to gain more control over the Hidden Leaf Village. He has no qualms about sacrificing others for his goals. Also, Kabuto could be a villain as he is a follower of Orochimaru and has his own motives for causing chaos.
In a 'naruto saves korra fanfiction', the villains could be a combination of different forces. There might be rogue benders who have turned to the dark side, using their bending abilities for evil purposes. These benders could be working with some mysterious outsiders who bring in new and unknown threats. Maybe there are ancient evils that have been awakened and they see Korra as a major obstacle. Naruto would then have to face these complex and dangerous foes to save Korra.
In this fanfiction, Jonathan is the central figure. His descendants, which could include a variety of individuals. There might be an older descendant who has preserved a lot of family history and is eager to share it with Jonathan. And there could also be a young, curious descendant who asks Jonathan a million questions about the past.
One of the descendants could be Giorno. Giorno has his Golden Experience Stand and is quite different from Jonathan in many ways. He's part of the new generation of the Joestar family. Also, Josuke could be among those he meets. Josuke is known for his Crazy Diamond Stand and his strong sense of justice, which he may have inherited in part from Jonathan.
Well, they might have an epic showdown at first. Jotaro with his Star Platinum and McCree with his Peacekeeper. But then they could realize they have a common enemy and team up. Maybe they'd exchange stories about their different worlds.
The Joker could be a likely villain. Imagine his chaotic nature combined with the supernatural. He might team up with a demon to create even more mayhem in both Gotham and Sunnydale. His unpredictable actions would pose a huge challenge to Buffy and Batman.