@bobbysq: Arceus supposedly created Dialga and Palkia, who created time and space respectively, dunno what Giratina does; Uxie, Mesprit and Azelf are allegedly responsible for knowledge, emotion and willpower; Groudon and Kyogre shaped the earth in a battle of land vs. sea, and Groudon must've been getting his ground-type ass whupped when Rayquaza made them cut it out, because just look at that water-to-land ratio.
I'm not fond of gen 3 and 4's legendaries for this, either. Gen 5's are considerably less pantheon-like and more legendary:
·Kyurem is the original dragon that came around during some kind of war, and split into Zekrom and Reshiram (normal Kyurem being its empty husk) when two twin brothers fighting for ideals vs. truth, neither could beat the other because Dragon/Fire and Dragon/Electric are type combinations that are fairly neutral to each other.
·After them we've got the musketeers, who don't really do anything but attempt to help a hero fight evil, or whatever.
·The genies, who are "forces of nature" but really just seem to be powerful ******bags with weather powers.
·Meloetta doesn't seem to have much of a reason to be a legendary at all, besides having a form gimmick. But then, so do Rotom and Darmanitan...
·Victini is thought to be an allegory for a nuke but is actually a living apple slice.
·Genesect is basically Mewtwo 2, being a powerful thing some
scientists decided "hey let's power it up more." Only instead of the scientists giving a Mew baby gene therapy, it was Team Plasma grafting cannons onto a prehistoric bug's back. I don't know where Plasma got any of the funding for their crazy shenanigans.
We can probably count on Xerneas and Yveltal being embodiments of good and evil.