In some fanfictions, a great plot twist is that the Legendary Pokemon raising Ash was actually sent by another group of Legendary Pokemon to balance the power in the world. So, Ash is like a key piece in a much larger power struggle. Another one could be that Ash's abilities, which he developed while being raised by the Legendary Pokemon, are actually a threat to some powerful forces in the Pokemon world. And they try to eliminate him. Also, a plot twist might be that the place where Ash was raised by the Legendary Pokemon is a secret dimension, and when he returns to the normal Pokemon world, he has to adapt to a world that is very different from what he knew while growing up.
One popular plot twist could be that Ash discovers he has a special power given to him by the Legendary Pokemon that raised him. For example, he might be able to communicate with all Pokemon telepathically. Another could be that the Legendary Pokemon that raised him is in danger, and Ash has to use his unique bond with it to save it from an evil organization. And sometimes, there's a twist where Ash's real family is somehow connected to the Legendary Pokemon world, and his upbringing by the Legendary Pokemon was part of a bigger plan to reunite his family.
Well, a common plot twist is when Ash's training under the Legendary Pokemon turns out to be a test. He thought he was just being raised, but in fact, he was being prepared for a much greater task, like saving the entire Pokemon world from a catastrophic event. Also, there might be a twist where the Legendary Pokemon that raised him isn't really what it seems. Maybe it was being controlled by a darker force all along, and Ash has to break that control. Another interesting twist could be that Ash is actually a reincarnation of an ancient Pokemon trainer related to the Legendary Pokemon, and his raising was to bring back the old glory of Pokemon training.