Alright, this might not be exactly what you're looking for, as it has a theme of Chaos and Order, rather than what you described in the original post, but I'll throw it out there anyway if anyone is interested. It is based on rival teams, similar to Team Aqua and Magma. My original setting for them is a northern snowy viking region, with legendaries based on norse mythology.
Central to the story is the strong will of one of the legendaries, capable of bending other life forms to its will, and the chaos affinity of the counterpart legendary, who's power can run entire societies to the brink of breakdown by turning people against each other.

Team Ataxia (Greek for "Lack of order") is a semi-religious group of fanatics, lead by a somewhat crazy leader (complete with crummy back and a wild grown beard) promoting anarchy and distrust for the government. The central thesis of Team Ataxia is that the world today has run its course and, corrupt as it is, there is no other way of saving society but to allow chaos to destroy civilization, and from the ashes rebuild a new world. To achieve this, Team Ataxia mean to use the power of the Chaos Pokemon and harness its power.
As a way to further pursue social disarray, Team Ataxia runs a crime syndicate to steal, release, and redistribute trainers' Pokemon.
The crazed leader is seldom accompanied with his admins and prefer to be alone, as he trusts no one, not even his closest to full extent, adding to the mystery of him. The admins see him as some sort of enlightened prophet and follows his word blindly, passing the orders along down to the grunts, who are doing the actual dirty work, often motivated by promises of further reward or promotions. The leader tries very hard to not become all that he strives to fight, but [might] end up

Team Axiom (From wikipedia: A starting point for reasoning) is the exact opposite of Team Ataxia.