I think Reshiram and Zekrom representing truth vs. ideals and the balance of society and nature was a pretty complex concept for Pokemon.
Though Rayquaza creating the atmosphere, Groudon creating the lands, and Kyogre creating the seas is pretty cool for Pokemon creationism. And how Regigigas pulled the continents together, Shaymin giving life to plants, Xerneas giving life to all creatures, and Mew being the starting point of modern Pokemon evolution bring it all together. It's really interesting putting those pieces together. It's a lot like Egyptian mythology.
