Well. I would imagine Aresus made Palkia and Dialga and Kyogre and Groudon, to shape the universe and the world, respectively. The two clashed, and thus, Rayquaza was made. The orbs were used to seal the pokemon away. Regigigas was born and helped bring the world together. Mew sprung up, evolving and branching outward into different species. I have a feeling the Regi Trio were born of human influence on the world, possibly through the developement of the technolog. They are golems, so I would imagine they were synthetically created by Regigigas, as the Golem, or Humunculus, was created from the earth and brought to life. Ho-oh soon developed or was pre-existing as far back as Aresus, or was created through the kindnesss of Man. A scenario similar to the Groudon-Kyogre conflict occurs amongst the birds of the three elements of destruction, and so a Lugia is born to balance the power, and the second time this happens was in the 2nd movie. Giranata represents the unknown mysteries of the universes and the afterlife. Darkrai maybe the End to Aresus's beginning, or rather, sprung up from the souls of those with negative energy. And... I can't think anymore.