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.
I think it would be Bran Stark. His ability to warg and see the past, present, and future is already quite powerful. If he were to gain a Stand on top of that, perhaps one that allowed him to manipulate time even more or have a stronger influence over people's minds while warging, he could potentially control the entire world of the fanfiction. He could see the moves of his enemies before they make them and counteract with his Stand powers.
Daenerys Targaryen might be the most powerful. Her dragons are already a huge advantage, but if she also had a Stand that enhanced her connection to them or gave her additional powers like mind control over her enemies, she could easily dominate. Plus, her charisma and claim to the Iron Throne would be boosted by these extra abilities.
It's hard to say for sure, but Thanos with the Infinity Stones could be extremely powerful. However, if we consider the JoJo universe, DIO with his time - stop ability and vampiric powers is also a force to be reckoned with. If they were to face off, it would be a battle of epic proportions.
It might be Ruby. Her speed and her scythe skills could make her a formidable opponent in the battlefields of Westeros. She could quickly move around and take out enemies before they even realize what's happening.
Well, it could also be argued that Daenerys Targaryen might be very powerful in such a fanfic. She has her dragons, which are extremely powerful weapons. If she were to enter Narnia, she could potentially use her dragons to gain a stronghold. However, she would still be no match for Aslan in terms of pure power and divine essence.
Perhaps Daenerys Targaryen. If she were to somehow acquire vampire - like abilities, she would be an even more formidable force. Her dragons combined with vampire powers such as enhanced senses and immortality (in a sense) would make her a very powerful and dangerous character. She could use her newfound powers to rule Westeros more effectively or to take on new enemies.
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.
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.
Well, some might argue that Aegon Targaryen with his dragon in Game of Thrones would be very powerful. But if we consider Fairy Tail, Acnologia, the dragon king, would be extremely powerful. If he were to enter the Game of Thrones world, he could easily destroy entire armies and fortresses with his dragon powers.
Klaus Mikaelson might also be considered the most powerful. His hybrid status gives him super strength, speed, and the ability to compel others. In the world of Game of Thrones, he could easily use his compulsion on many of the characters to get what he wants. He's also very difficult to kill, which would give him an edge over most characters from Game of Thrones.
Arya Stark with Elder Scrolls training could be a very powerful combination. If she learned the ways of stealth and assassination in Elder Scrolls, combined with her already impressive skills from Game of Thrones, she could become a deadly assassin. She could use Elder Scrolls - style magic to enhance her stealth and take out her targets more effectively.
However, Voldemort also has a claim to being the most powerful. His dark magic is extremely potent, and if he were to enter the Game of Thrones world, he could use fear and intimidation to gain power. He might even form alliances with some of the more ruthless characters in Westeros to achieve his goals.