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Event-exclusive Pokemon are banned, presumably because it puts new players at a disadvantage (as they were not able to obtain the event Pokemon when they didn't have the game).
Other legendary Pokemon are allowed because they can be obtained through the game by normal means. Generally limits are placed on Mewtwo and the box-art legendaries since they all have a higher BST than pretty much every Pokemon. The other legendary Pokemon are theoretically no stronger than pseudo-legendaries because they have the same BST.
