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Here's where I'd put them in the hierarchy.
Arceus and the creation trio on top are obvious.
Solgaleo and Lunala are beneath Palkia because the sun and moon exist in space.
Zygarde is the guardian of the Earth, which also exists in space, so it's beneath them as well.
Weather trio is beneath Zygarde because there's now land, sea, or sky with no Earth.
Landorus is beneath Groudon because it's guardian of the land, and the entire genie trio is beneath Rayquaza because they're all part of weather.
Shaymin is beneath Landorus because plants and nature and shit exist on the land that Landorus cultivates.
Regigigas merely moved the continents while Groudon created them, so Regigigas is beneath Groudon.
The Tapus and Calyrex are beneath Regigigas because they're rulers over a piece of land, and Regigigas is the one who decided where the land should be.
Xerneas and Yveltal are beneath the weather trio because life and death require the land and sea and sky to exist.
Mew is beneath Xerneas because it's the common ancestor of all Pokemon while Xerneas is the ruler over life itself.
Lake trio is beneath Mew because there's no consciousness without life.
Swords of Justice and Dream duo are beneath Lake trio because there's no justice or dreams without consciousness.
Ho-Oh is beneath Mew because it can restore lost life, but can't create new life.
Humans and Pokemon were once the same, so humans are also descendants of Mew, and therefore any manmade Pokemon are ultimately derivative of Mew.
Other than that, I think the rest are self-explanatory. I have no idea where the Lati twins fit in the grand scheme of things, though. Not sure if they're from space or if they're just powerful creatures.
