It could be a powerful Team Rocket member who has a personal vendetta against Kid Silver. Maybe he's jealous of Silver's natural talent with Pokemon.
Perhaps a new evil organization could be the main antagonist. They might be trying to capture all the shiny Pokemon for some dark purpose, and Kid Silver stands in their way. This organization could have some really strong and unique Pokemon that Kid Silver has to battle against. They could also be led by a mysterious figure who has a hidden past related to Silver's family or something like that.
It could also focus on Kid Silver's relationship with his Pokemon. For example, he has a special bond with a Pikachu that he found as a Pichu. Together, they overcome difficulties and prove themselves to be a formidable team in the Pokemon world. He might enter Pokemon contests with his Pokemon as well, showing off their unique skills and abilities.
An organization of rogue scientists who want to experiment on Pokemon could be the main antagonist. They might be trying to create super - powerful mutant Pokemon or find a way to control all Pokemon. If you're reborn as a Pokemon, they might capture you for their experiments. This could lead to a story where you have to escape from their labs and expose their evil plans to the rest of the Pokemon world.
Dr. Eggman could be a great antagonist. He might be creating a new weapon or device that could disrupt the balance between time (which is relevant to Silver) and space (relevant to Shadow). His actions force Silver and Shadow to work together to stop him.
It could be a powerful Grimm that has a special connection to the character in the trailer. Maybe this Grimm has been hunting them for a long time and is finally about to catch up.
The main antagonist could be a powerful trainer who has been banned from official Pokemon leagues for using underhanded tactics. In the Game of Champions, he sees an opportunity to regain his reputation and will stop at nothing to win. He uses his knowledge of Pokemon psychology to manipulate his opponents' Pokemon during battles.
A new, mysterious organization that is interested in controlling the legendary Pokémon. They see Latias as a key to their plan and Ash as an obstacle to be removed.
A powerful and corrupt Pokemon trainer who wants to use rare Pokemon for his own evil plans could be a great antagonist. He might try to steal Pokemon from Wes and Rui or stop them from achieving their goals.
Perhaps an evil Pokémon organization. They could be conducting unethical experiments on Pokémon, and when they hear about the reborn Pokémon, they want to capture it for their research. They might believe that the reborn Pokémon holds the key to some sort of ultimate power or knowledge that they can use to take over the Pokémon world.
A powerful and greedy trainer who wants to capture Manaphy for its rare abilities could be the main antagonist. He might have a whole team of strong Pokemon and use underhanded tactics to try and get Manaphy.
It could be Team Rocket. Since they always cause trouble for Ash in the original series, in this fanfic, they might see Ash's transformation into a Pokémon as an opportunity to capture him and use him for their evil plans.