If Groudon/Kyogre/Rayquaza's "mega" forms are their "original" forms, then maybe all megaevolution of Pokemon are from a state of their original forms. Maybe there can be a hidden lore element of having an "era of gods" where ancient Pokemon were huge, humans hid underground, and this all changed after some catastrophe 3,000 years ago, and Pokemon "evolved" to the modern form, which conserves energy