It could be the Scarlet Witch. Her reality - warping powers are off the charts. In a Game of Thrones setting, she could literally change the landscape, turn armies against each other, or even create illusions on a massive scale. She could make a whole castle disappear or make an army think they are being attacked by dragons when there are none. Her powers are not bound by the rules of Westeros' magic, so she could be extremely dangerous and powerful.
Black Widow. She's a master spy and assassin. In the world of Game of Thrones, she could easily blend in with the various spies and informants. She could play the game of thrones better than most of the characters there, using her charm and combat skills to manipulate the situation to her advantage. She might even be able to uncover some of the deepest secrets of the Seven Kingdoms.
I think Iron Man and Tyrion Lannister would be a really interesting pairing. Iron Man is this brash, genius billionaire, and Tyrion is the clever, outcast dwarf in Westeros. They could bounce ideas off each other, with Iron Man showing Tyrion his high - tech gadgets and Tyrion teaching Iron Man about the political games in Westeros.
It could be Arya Stark. In Game of Thrones, she has proven to be a highly skilled assassin. In a Mortal Kombat crossover, her ability to change faces and sneak up on her enemies would be a great advantage. She could use her Needle sword and her skills learned from the Faceless Men to take on opponents. And her list of names of those she wants to kill could easily be added to with Mortal Kombat villains.
In my opinion, it could be Scarlet Witch. Her reality - warping powers are extremely potent. In a crossover, she could potentially change the very fabric of the combined universes. If she were to go rogue or be influenced by an evil force, she could cause chaos on a scale that would be very difficult for the combined might of the Justice League and the Avengers to handle. Even Superman's invulnerability might not protect him from her reality - warping abilities. She could simply make him mortal or take away his powers altogether.
It could be Jon Snow. If he has a Stand in the fanfiction, combined with his already proven leadership skills and combat abilities, he would be a force to be reckoned with. His ability to come back from the dead might also be related to his Stand powers in some way, making him even more formidable.
Thor would be very powerful. He has his hammer and lightning powers. Against the dinosaurs, he could easily zap them with lightning or use his strength to fend them off. He could also fly around the Jurassic World area, which gives him an advantage in terms of mobility.
It's hard to say. Thor has his godly powers and Mjolnir. But Percy can control water and has defeated many powerful monsters. It could be either depending on the situation.
Ultimately, it depends on how the crossover is written. If it's a story that focuses on technological superiority, then Iron Man or some of the more tech - savvy Avengers could be the most powerful. They could create new weapons or devices that give them an advantage. But if the story is more about spiritual and magical powers, then the Jedi and Sith would likely be the most powerful. For example, if the story is set in a way that the Avengers have to adapt to the rules of the Star Wars universe, then the characters who can quickly master the Force would be the most powerful.
Jon Snow would also be a great addition. His journey from being a bastard to a leader in Game of Thrones could be paralleled in the world of Frozen. He could learn from Elsa about controlling his powers (if we assume he has some new ice - related powers in this crossover) and in turn, teach the people of Arendelle about loyalty and sacrifice, which are values he has held dear in Westeros.
Arya Stark in a 'Naruto Game of Thrones crossover fanfiction' would be fascinating. If she were to learn some of Naruto's ninja skills, she would become an even deadlier assassin. And Naruto's influence might change her path a bit, making her less vengeful and more about bringing real change to Westeros.