As interesting as this concept is, what you propose is similar to a holy war. I'm not sure that's something Pokemon wants to tackle.
holy wars are ambiguous. the mass extinction dealt with in XY would be almost unanimously recognized as bad. i don't think holy war would necessarily be off the table, although it would likely take a lot of Plasma-esque writing which i'd say isn't all that ideal.
I'm gonna step back and say I don't actually see how the idea @tyguy723 proposed is similar to a holy war at all. I mean, why isn't the conflict between Team Magma and Team Aqua a holy war? It's for power but it's also based on their beliefs that there should be more land/water. And just having the two "clans" competing to summon their own legendary sounds more, as I just said, like a competition, not a war. Especially if they DON'T have malicious intent like previous teams had. Continuing with the idea, I could see the Clan Leaders or whatever meeting each other, or opposing clan members meeting each other, without any animosity between them. Sure, they want different things, but that doesn't mean they have to hate each other or want to kill each other, or even battle each other. (On a side note, we all know Maxie and Archie DEFINITELY don't hate each other )
Anyway I liked the idea, but I think it won't happen for another reason; defeating the big bad is a better story for a younger audience. At least I think so....