...wait. Base Rayquaza stopped both Primals? With no evolution? And then when the bigger meteor fell, people prayed and it Megaevolved even though there was no threat?
Yeah, Rayquaza Mega Evolving was more of a fortuitous coincidence. The people prayed hoping that it would appear like it did a thousand years before, and it did. But this time, they prayed next to what was essentially a giant Key Stone, and that caused their feelings to resonate with Rayquaza’s mikado organ, inducing its Mega Evolution. Narratively speaking, it’s more important for the symbolic power of the moment, rather than the literal increase in power that Rayquaza had compared to the last time.
That being said, I think there is an implied difference in the end — in Zinnia’s story, when she talks about the first incident, she merely says that Rayquaza “overwhelmed” Kyogre and Groudon, but during the second incident, she says, “The wind and emerald light visibly sapped the power from Primal Groudon and Primal Kyogre. Drained of their primal powers, the two vanished into the depths of land and sea.” And when we find Groudon/Kyogre in ORAS, they’re down in the Cave of Origin, completely still and colorless.
I think it’s possible that Mega Rayquaza sapped
so much power from them that there wasn’t a chance of them ever waking up again without some serious external stimuli (in this case, being exposed to the Red/Blue Orb that contains their power). Although we obviously can’t encounter the opposite Legendary for exclusivity reasons, I think we can read some narrative into its absence as well.
Clearly, both Groudon and Kyogre exist in the world regardless of whether you’re playing Omega Ruby or Alpha Sapphire, because they both appear in the legends. But 1,000 years ago, when the meteorite struck Sootopolis, the release of energy caused them both to wake up, since they’d only been quelled by regular Rayquaza before. But in the present, the giant release of energy from the Cave of Origin that occurs after Groudon/Kyogre (solo) is dealt with
doesn’t cause the other Legendary to appear — because they’re still frozen in place somewhere, devoid of all energy due to what Mega Rayquaza did, and without Team Magma/Aqua trying to revive them in that version of reality, there they will remain for the foreseeable future.
Is the DLC necessarily post-game? If it is then we got the pretext for the new Megas there, if it isn't then they just got an excuse for future new Megas.
On top of what R_N said about there still being plenty of wiggle room for new Mega Stones created by the weapon’s use in XY to be discovered, there’s also another the additional possible layer of “Are these Mega Stones only found in Hyperspace Lumiose, and not normal Lumiose?” They could be special
~alien~ Mega Stones with no connection to the ultimate weapon or to Ange.