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since mewtwo has 2 different megas that are version exclusive, there is strong evidence that suggests that yveltal and xerneas play a large role in its mega evolution.
First, look at mega mewtwo's eyes. mega mewtwo x has blue eyes while mega mewtwo y has red eyes. this shows how mewtwo is being influenced by the power of xerneas or yveltal, respectively.
Furthermore, examine Xewtwo's body structure. it seem's to be of a more guardian like build, as if meant to be the guardian of life itself. Its ability steadfast and its fighting typing (which usually signifies honor and dignity). It is also more ground-based and natural, similar to xerneas.
Now look at Yewtwo. Its small stature and horns give it almost a demon-like vibe. Its frailty symbolizes death itself, with yewtwo being the harbinger of death, using long ranged attacks to rain destruction upon life. Its ability insomnia seems to be a reference to how 'death never sleeps'.
Thoughts?