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Mewtwo is a character. Every other legendary is a plot device; an animated universal abstract -- fire, ice, thunder, water, air, earth, nature, magic, technology, darkness, yin, yang, wuji, logos, ethos, pathos, space, time, creation...
These are cool, but they're constant. These are things that always have been, always will be, and always must be, or else nothing could be. They exist to do the perpetual, Sisyphean, vital work of the cosmos. Thus, they can't change, and can't have a character arc, and can't be strong characters.
Mewtwo, on the other hand, is created in absence of a role, and is subject to all the existential uncertainty, conflict, folly, resolve, achievement and ultimate growth therein.
Basically, every other legendary is the world around us, and Mewtwo is our experience within that. Mewtwo is us.