For a main character from the human side, it's Michael Rosen. And from MLP, I think Rarity could be a main character. Rarity would be fascinated by Michael Rosen's different style of dress (compared to ponies) and might try to create pony - versions of his outfits. And Applejack could also be a main character, showing Michael Rosen how to work on the farm and sharing her values of hard work and honesty with him.
Well, it could be about Michael Rosen getting transported into the MLP world. Maybe he starts out confused but then uses his storytelling skills to help the ponies solve a problem like a drought or a conflict between two pony tribes. He could tell stories to cheer up the ponies during a tough time.
Once upon a time, Michael Rosen found himself in the Mushroom Kingdom. Mario was on a mission to rescue Princess Peach as usual. Michael, being his curious self, decided to tag along. He started telling his famous stories to Mario as they hopped over the mushroom platforms. Mario was initially confused but soon found the stories quite interesting and it gave him new energy to face the challenges ahead. Together, they defeated Bowser in a rather unconventional way. Michael used his words to outwit Bowser while Mario did the physical fighting.
Imagine that Michael Rosen is from a parallel dimension where everything is made of words. When he enters Mario's world, he starts to turn the enemies into harmless words. Bowser, seeing this as a threat, tries to stop him. Mario and Michael team up. Michael uses his word - changing ability to weaken Bowser, and Mario gives the final blow. In the end, they learn from each other and Michael returns to his word - dimension, but not before leaving behind some magical word - seeds that grow into beautiful story - trees in the Mushroom Kingdom.
Godzilla himself would obviously be a main character. His actions and reactions would drive much of the story. Another possible main character could be Pinkie Pie. Her unique view of the world and her ability to make friends with anyone could play a role in how the ponies deal with Godzilla. Maybe she throws a party for Godzilla to make him feel welcome.
Riku could also play a major role. His more complex and sometimes brooding personality could add an interesting dynamic. He might start off as a bit of an outsider in Equestria but eventually come to understand and care for the ponies, especially if there are some ponies who remind him of his friends from his own world.
Link and Twilight Sparkle would be obvious main characters. Link with his skills in combat and exploration, and Twilight Sparkle with her powerful magic and intelligence. They could form an unlikely duo to face challenges.
Twilight Sparkle could be a main character. Since she is very intelligent and curious, she might be the one who gets drawn into the Creepypasta - related events. Her knowledge of magic could also play a crucial role in either solving the problems caused by the crossover or in getting trapped in the first place.
His best friend could be a key character. This friend could be the one who was with him when he got burned and feels guilty about it. So, the friend tries to make it up to Michael by being extra helpful during his recovery, bringing him things he needs and just being there for him to talk to.
A powerful dark wizard from the human world who has found a way to cross over into Equestria. He wants to harness the magic of the Elements of Harmony to increase his own power. He sees the Ghost Rider as a threat to his plans and tries to eliminate him while also causing chaos in Equestria.
It could be that Fluttershy is one of the main characters. Given her gentle nature, she might be drawn to the Phantom, thinking she can help him. And of course, the Phantom is a key character. There could also be a new pony character created specifically for this fanfiction, who has a special connection to the Phantom and the events of the story.