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I think it would have been more impactive on the player if they also showed Celebi, Jirachi, Ampharos, and Espurr getting turned into stone. We know that even Raikou, Entei, and Suicune get tired at fighting shadows, but seeing Mega Mewtwo Y, Arceus, Deoxys, and Mega Rayquaza getting swamped by them would be something else.
It would have been fucking hilarious if it showed Cofagrigus, Kecleon, Hawlucha, and Klefki getting turned into stone at the guild. I don't even think you can use any of that stuff without Pelliper Island once you reach the roots of the tree.
btw how does multitype work in super mystery dungeon