I noticed something strange in ORAS.
By replaying very recently the game, they made few change that seem insignifiant at first, but now makes a whole new sense. I am talking about RSE versus ORAS, and how they tied it together with what we know in X/Y and possibly the future.
1. Shelly, the admin of team aqua, now has a back story that she used to work at devon corp, which create product based on the infinie energy.
So she has a background as a scientist and for some reason joined team aqua....
2. Both her and the other aqua leader, have their skin color changed in the remake, including the leader Archie.
They are all tanned, now look at the anime representation or what they where in RSE, they where all white, now kinda brown like.. people that comes from island.(like aloha)
http://bulbapedia.bulbagarden.net/wiki/Aqua_Admin_Matt3. She also seem to be very closely related to the leader in a personal way, they probably living together before or are in couple, they have the same ambition.
4.Courney mention in the delta episode that she want to fix the AZOTH project, by destroying the metorite and the world, both the ultimate plan of magma/aqua are actually altered in the remake to be some sort of reboot of the world without humain intervention/while the other is expanding civilisation or humain progress. It's no longer just having more land or more water.
5. The 2 leader of those team where mentionned to be part of an original team, this did NOT exist in RSE.
The things is i suspect them to be part of something greater, that actually understood what natural energy is, and how to make the world a better place(possibly Aether) So their difference is actually a split of ideology from the same source.
In their base not only you find doc about about Azoth, but also the difference between primal evo/Mega evolution?
I just have the feeling that Aether is the great source for most of the deviation of the evil team that took their own interpretation.