Jon Snow might be a strong contender. He has come back from the dead in Game of Thrones, which could give him an edge in Mortal Kombat. His Valyrian steel sword, Longclaw, can defeat the undead in his own world, and it could be very effective against Mortal Kombat foes. Also, his leadership skills and experience in battles could make him a force to be reckoned with in the crossover.
Sauron from Mortal Kombat could be extremely powerful in this crossover. He has powerful magic and is a very intimidating figure. In a world where the rules of both universes apply, his ability to control and manipulate could be a huge threat. He could easily turn some of the Game of Thrones characters against each other with his mind - control powers, and his physical strength in combat is also very high.
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.
It could be Akuma. His Satsui no Hado gives him incredible power and his fighting skills are top - notch. In a crossover, he could easily adapt to the Mortal Kombat's more brutal fighting style and use his dark powers to overpower many opponents.
It's really hard to say for sure. Shao Kahn from Mortal Kombat is extremely powerful with his brute strength and magical abilities. But then you have characters like M. Bison from Street Fighter who has powerful psychic powers. If we consider a crossover, it might depend on the rules of the world they are in. In a world more based on Mortal Kombat's rules, Shao Kahn might have the edge, but in a more Street Fighter - like setting, M. Bison could be more dominant.
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.
Well, Raiden from Mortal Kombat might be a strong contender. He is a thunder god with incredible powers. In a crossover with Harry Potter, his ability to control lightning could give him an edge. He could use his powers to disrupt the magic of wizards or directly attack them. And his immortality would make him a difficult opponent to defeat, even against the most powerful wizards.
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.
The use of magic and supernatural elements. In Game of Thrones, we have things like the White Walkers and dragon magic. In Mortal Kombat, there are things like the Elder Gods and their magic. Fanfiction can explore how the magic from both universes could interact. Maybe the dragons in Game of Thrones could be used in Mortal Kombat - style battles, or the Elder Gods could have some influence on the events in Westeros. It opens up a whole new realm of possibilities for the story.
Scorpion from Mortal Kombat could be a very interesting character in this crossover. His hellish powers and his quest for revenge could put him at odds with some of the Naruto characters. His battles with Naruto or Sasuke would be intense, especially with his ability to teleport and use his kunai chain.
Another strong contender could be Raiden. As a thunder god in Mortal Kombat, he has control over lightning and has great combat skills. In the Harry Potter universe, his lightning attacks could be very difficult to defend against. He could also use his powers to disrupt magic, as electricity can interfere with magical devices. His immortality also gives him an advantage, as he can keep coming back in a fight no matter how much damage he takes.
Scorpion would be very interesting. Scorpion has a tragic backstory and his hellish powers are a great contrast to Kenshi's more earthly - based sword and telekinesis skills. Their interaction could be full of tension at first, as Scorpion is often distrustful, but they could learn from each other and become a powerful force. For example, Scorpion could teach Kenshi some of his stealthy combat moves, while Kenshi could show Scorpion how to better control his rage using telekinesis.
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.