Sonic would definitely be one of the main characters. His speed and heroic nature would make him a key figure in any crossover. Also, Freddy Fazbear from FNAF would be important as he is sort of the face of the FNAF franchise. Sonic could be the one trying to find a way out of the FNAF world or stop the animatronics, and Freddy could be the character that Sonic has to either defeat or befriend in order to achieve his goal.
Eggman Nega could be a great main antagonist. He has the intelligence and the desire for power. He could find a way to open portals between the Sonic X and Sonic Boom universes to steal resources and technology from both. His plans would force Sonic X's Sonic and Sonic Boom's Sonic to team up against him. He could use his robotic creations from both universes, combining the advanced tech from Sonic X and the more rustic, yet effective, machines from Sonic Boom.
Dark Matter could be the main antagonist in this crossover. Dark Matter is a powerful and menacing force in Kirby's world. In the crossover, it could have somehow found a way to cross over into Sonic's world and is corrupting it. Sonic and Kirby have to find a way to stop Dark Matter from spreading further. Dark Matter tries to use Sonic's speed against him by creating dangerous obstacles in his path and Kirby has to use his various powers to help Sonic overcome these while also directly fighting Dark Matter.
Obviously, Harry Potter himself could be a main character. He has the experience of dealing with dark forces, so he would be likely to take on the mystery of the FNAF animatronics. Hermione Granger would also be a key character as her knowledge of magic and books could help in understanding the situation. Maybe Freddy Fazbear could also be a sort of main character on the FNAF side, being the leader of the animatronics.
Harry Potter himself could be the main character. He has the experience of dealing with all kinds of dark and strange things, so he would be a natural fit to face the FNAF animatronics in the crossover. He could use his magic skills like the Patronus charm to fight against any dark influence the animatronics might have.
A brand - new character could also work well. Imagine a powerful sorcerer from a different dimension. This sorcerer has the ability to manipulate time and space, which would put both Shadow and Silver at a disadvantage. He could be after Sonic's chaos emeralds to increase his own power and spread his dark magic across all the Sonic universes.
One idea could be that Sonic and his friends accidentally end up in the FNAF universe. Sonic's speed could be a huge advantage against the animatronics. For example, he could quickly dash around the haunted pizzeria, confusing the animatronics and leading them into traps. Another idea is that the animatronics from FNAF somehow get transported to Sonic's world. The chaos that would ensue as they try to adapt to the bright, colorful and fast - paced Sonic world would be really interesting to write about. Maybe Sonic and Tails would have to figure out a way to send them back while also protecting their friends from the animatronics' unpredictable behavior.
Obviously, Sonic would be one of the main characters. He'd bring his high - speed action and adventurous spirit. Twilight Sparkle from Legend of Everfree could also be a main character. She's intelligent and has powerful magic. They would make an interesting duo, with Sonic's physical abilities and Twilight's magical ones.
Probably Leonardo from the Turtles and Freddy Fazbear. Leonardo is the leader, so he would likely be the first to step forward and assess the situation when they encounter the FNAF animatronics. Freddy, being the main animatronic, would also be in the forefront. Their personalities are quite different, with Leonardo being more disciplined and Freddy having a more mysterious and somewhat menacing presence. Their first interaction could be a tense stand - off as they try to figure out each other's intentions.
Tails would be an obvious choice as he is already part of Sonic's world, but if we think outside the box, characters like Spider - Man could be great. Spider - Man's acrobatic skills and Sonic's speed would make for an exciting team - up. They could swing and run through New York City together fighting crime.
Bonnie from FNAF could be a great crossover character with Foxy. They already have a connection in the FNAF universe, and in a crossover, they could have new adventures together, perhaps in a different time or place.