maskofsanity1998
Rebel
I'm further developing this good plot you have: let's say in Alpha Sapphire, Team Aqua attempt to awaken Kyogre, while the opposite team, Team Magma, tries to help you awaken Rayquaza in order to neutralise the weather and neutralise Team Aqua's plan. Team Aqua are thwarted as per Sapphire, and Kyogre flees to Marine Cave as happened in Emerald, not able to be caught until post-story and out of the picture. But then it turns out Team Magma have just been using you and hiding their true motive, which was to use Rayquaza to get Team Aqua out of the equation, so they can kidnap and neutralise Rayquaza themselves, and by that it would allow Groudon to be completely undisputed in their plot to create more land mass.
Obviously switch Aqua/Magma and Kyogre/Groudon for Omega Ruby.
We'll have a full plot worked out between us all yet!
forget gamefreak, we got this! or rather you guys got this, I haven't helped much