Amy could be a central character. Given her caring nature, she would be the one most likely to take care of baby Shadow. Rouge would also be important as she has a connection with Shadow. She might be the one who first discovers Shadow in his baby state and then alerts the others. Knuckles could play a role too, perhaps protecting the place where baby Shadow is being taken care of from any potential threats.
Obviously, Shadow himself would be a main character even in his baby form. Sonic would also be a key character as he is often the hero in these Sonic - related stories. He would likely be involved in trying to figure out how to turn Shadow back. Tails could be another main character as his intelligence would be useful in finding a solution to Shadow's transformation. He might study the cause of it and try to come up with a remedy.
One possible plot could be that some sort of strange chaos energy experiment goes wrong. Shadow is caught in the blast and suddenly transformed into a baby hedgehog. Sonic and his friends find him in this state. They then have to take care of him while trying to find a way to reverse the transformation. They might face challenges like protecting baby Shadow from Eggman who could see this as an opportunity to get rid of Shadow once and for all.
Obviously, Shadow the Hedgehog is a main character. He's the one with the vampire - like qualities. Sonic could also be a main character in some fanfictions. He might be in conflict with Shadow because of his new vampire nature or could be trying to help him control it. Amy could be another main character, perhaps she has a special connection to Shadow and tries to understand his transformation.
Obviously, Ash would be a main character even in his baby form. Pikachu is bound to be a key character as well, being Ash's closest Pokémon partner. His other Pokémon like Bulbasaur, Charmander, and Squirtle could also play important roles in protecting and taking care of baby Ash.
Maybe the main antagonist is a scientist who has been experimenting with vampire-like powers and accidentally creates a powerful vampire - like monster. This monster then starts attacking the world, and Shadow, as a new vampire - hedgehog, has to stop it. The scientist might also be trying to cover up his mistake and will stop at nothing to keep Shadow from interfering.
Obviously, Baby Shadow and Maria are the main characters.
Mario would definitely be a main character. Since Luigi is his brother, he would be the one most concerned about Luigi's transformation and would do everything he could to help him. Princess Peach could also be a main character. She might offer her castle as a safe place for baby Luigi and use her resources to find a solution. Toad could be there too, helping Mario with taking care of Luigi and providing useful information about the kingdom that could lead to reversing the spell.
Perhaps a mysterious stranger. This stranger could have some connection to the reason why Edward turned into a baby. And then there's Edward's pet dog. The dog might be confused at first but then becomes very protective of baby Edward, adding an interesting dynamic to the story.
Her best friend could be a main character. They might be the one who is most affected by her transformation and has to take on a lot of responsibility in taking care of her.
Erza could also be a main character. Given her strong and motherly side, she would probably take on the role of taking good care of baby Lucy. She might be strict about following a routine for baby Lucy's care. Happy, the flying cat, could be another important character. He could use his unique abilities to search for clues on how to turn Lucy back to normal.
His guildmates would surely be main characters. For example, Natsu could be there. Natsu might be really confused at first but then would be super protective of baby Laxus. Another could be Lucy. She might be the one who is more practical in taking care of the baby, like making sure he has proper clothes and a comfortable place to sleep.