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.
Zelda and Princess Celestia could also be main characters. Zelda is known for her wisdom and connection to the Triforce of Wisdom. Princess Celestia has great power and leadership in Equestria. Together, they could lead the fight against any common threats that emerge from the crossover, like a new villain that combines elements of both universes.
Another possibility is that Ganon and Discord could be main characters, but in an antagonistic role. Ganon, the great evil from The Legend of Zelda, and Discord, the chaos bringer in MLP. Their combined malevolence could create a huge crisis that forces the heroes from both universes to come together and stop them.
It could be about Link ending up in Equestria and teaming up with Twilight Sparkle to fight a new evil that threatens both their worlds. Maybe Ganondorf has found a way to enter Equestria and is causing chaos, and Link uses his combat skills while Twilight uses her magic to drive him out.
The characters could interact through shared quests. For instance, if there's a dark force emerging in both worlds, they might work together to defeat it. Link could teach the ponies some combat skills like sword - fighting (maybe in a pony - friendly way), and the ponies could teach Link about their unique magic and how it works in Equestria.
One idea could be that Link, the hero from Legend of Zelda, somehow gets transported to the world of MLP. He might team up with Twilight Sparkle to fight against a common enemy that threatens both their worlds. Maybe Ganon has found a way to corrupt the magic in Equestria, and Link's combat skills along with Twilight's magic knowledge are needed to stop him.
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.
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.
Mario would be a great character to include. He's from a very different game world, and seeing him interact with Link could be really fun. Another good one could be Sonic. His speed and Link's combat skills could make for an interesting combination.
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.
One option for the main character is an OC (original character) who has the spirit of Naruto inside him but looks like Link. He has the determination of Naruto and the adventuring skills of Link. In the harem, we could have Ino from Naruto. She's confident and has her mind - related jutsus. And from Zelda, Midna could be a part of it. She is a complex and powerful character. Another character could be Hinata. Her shy yet strong nature would add an interesting dynamic to the harem.
There are three main characters in the Legend of Zelda story. Firstly, Link, the brave hero. He is the one who goes through all the challenges and battles. Then, there's Princess Zelda. She is not just a damsel in distress. She has a significant role in the story as she is linked to the Triforce. And of course, Ganon, the villain. He is always trying to gain power and take over Hyrule, which makes him the main antagonist that Link has to face.