I think Voldemort and Fluttershy would be a really unexpected pairing. Voldemort is all about power and darkness, while Fluttershy is the shy and gentle pony. It would be very strange to see how they interact if they were in the same story.
Twilight Sparkle and Hermione would make an interesting pairing. Both are highly intelligent and love to study magic. They could have long discussions about different spells, magical theories, and how magic works in their respective worlds. Another good pairing could be Rainbow Dash and Harry Potter. Rainbow Dash is brave and fast, just like Harry, and they could team up to face some sort of danger, like a dark wizard who has found a way to enter Equestria.
It has to be Spike. He's a small dragon in the My Little Pony world. In Mortal Kombat fanfiction, he could use his ability to breathe fire in really creative ways. He could also use his small size to his advantage, sneaking around and attacking from unexpected angles. His loyalty to the ponies would make him a really determined fighter, which would be quite unexpected considering his usually cute and helpful role in the pony world.
Definitely Harry Potter and Twilight Sparkle. Harry is used to dealing with dark magic and saving the wizarding world, while Twilight is all about learning and magic in Equestria. They could share their knowledge of different types of magic and work together to solve problems. For example, when facing a powerful dark spell, Harry's experience with the Patronus charm could combine with Twilight's spell - casting skills to create a new form of defense.
I think Luna from My Little Pony and Severus Snape would be quite interesting. Luna has her own struggles with her past and redemption, much like Snape. Their brooding natures could lead to some very deep and complex conversations, perhaps about forgiveness and second chances.
Perhaps Dwight Enys from Poldark and Arya Stark from Game of Thrones. Dwight is a healer and a man of science in his world, while Arya is a trained assassin. The idea of them coming together, with Arya maybe getting some medical help from Dwight or Dwight learning some of Arya's survival skills, would be quite unexpected and could lead to a unique fanfiction plot.
One interesting concept could be the magic systems combined. Maybe the wizards from Harry Potter could interact with the unique magic of the My Little Pony world. For example, they might learn about the harmony magic that the ponies use.
The Hulk and Neville Longbottom. It seems really odd at first because the Hulk is this big, powerful brute and Neville is often seen as a bit of a clumsy underdog. But Neville has a lot of hidden courage. In a battle, the Hulk's brute strength combined with Neville's new - found confidence and knowledge of magic could be a really unexpected and powerful alliance.
I think Harry Potter and Bugs Bunny would be a really interesting pairing. Harry has his serious and determined nature, while Bugs is all about being quick - witted and comical. They could work together to solve a mystery at Hogwarts. Bugs might use his tricks to distract the bad guys while Harry uses his magic skills to defeat them.
I think Darkseid would be the most unexpected. Imagine Harry Potter being raised in Apokolips. He would have to adapt his magic to survive in such a harsh and evil - dominated place. His magic could potentially be a threat to Darkseid's rule, or he could learn some dark magic - like powers from Darkseid's regime, which would completely change his character and the way he uses magic.
The most unexpected pair to switch in 'Harry Potter Freaky Friday' fanfiction could be Neville and Bellatrix. Neville, who is kind - hearted and a bit clumsy at times, would suddenly be in the body of the cruel and powerful Bellatrix. Bellatrix, in Neville's body, would have to deal with Neville's insecurities and his new - found courage which would be a huge contrast to her normal self.