Thanos is a likely one. Given their both having grand ambitions in the Marvel universe. In fanfiction, their meeting could be a battle of wills as they both want to be the dominant force. Loki might initially try to deceive Thanos, but Thanos is no fool and would see through Loki's tricks.
Doctor Doom could also be one. He is a powerful and intelligent villain. If Loki meets him, they could have an exchange of knowledge. Doom might be interested in Loki's magic, and Loki could be intrigued by Doom's scientific and magical hybrids. Their encounter could be filled with a lot of posturing and attempts to one - up each other.
He could meet the Frost Giants. Since he has some connection to them already, they might welcome him or at least be intrigued by his presence. He could learn more about his heritage from them and maybe even form an alliance.
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.
One likely antagonist could be Thanos. He is a powerful and menacing villain who wants to collect all the Infinity Stones. His goals would put him at odds with both Loki and Tony. Loki might have been manipulated by Thanos in the past, and Tony would be against Thanos' plan to destroy half of the universe.
Thor would be a likely candidate. Since he is Loki's brother, he already has a connection with him. Thor might be the one to convince the other Avengers to give Loki a chance and be the first to reach out and try to befriend him in this new situation.
I think it could be Star - Lord. He's often looking for an edge in any situation, and Loki could offer some unique opportunities. They could form a sort of uneasy alliance where they both try to use each other for their own goals. Star - Lord might see Loki as a valuable asset in terms of his magic and knowledge of other worlds, while Loki could use Star - Lord's leadership skills and connections within the Guardians. However, they would constantly be on guard against each other's double - crosses.
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.
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 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.