As much as I am a cheap bastard, Game Freak are greedy bastards. I wouldn't be surprised if you were right - they used Emerald's storyline/teams. . . But then only let you catch Groudon in OR and Kyogre in AS.
If you're not expecting version exclusive Legendaries, you're doing it wrong.
"But... but... Internet era! Patch!"
Nope. If they had planned to do that, they wouldn't have included the dozen-odd "hidden moves" in XY. Thousand Arrows, Thousand Waves, Light of Ruin... all of those were added to XY, so they could be used by event exclusive Pokémon without the game breaking. Had GameFreak planned on making new moves for ORAS, they would have been hidden on the XY cartridges already. If they had decided to rely on patches, there wouldn't have been any hidden moves on the cartridges at all. They too would have been introduced by patch, instead of being put on the cartridges upon release.
I'm sorry but I just don't subscribe to this view.
We are essentially in uncharted territory here as no previous gens had Mega Evos that REQUIRE a specific item to occur, and all games of a Generation need to be compatible with each other in some form or another.
For all you and I know, there could be a patch download required, or there could be a compatibility patch that your copy of OR/AS will send to X/Y should a local battle occur.
We've seen the DS generation of games able to send quite complicated info to each other (Mario Kart multiplayer comes to mind, plus there was the interaction between 2 DS machines on the Poketransfer lab) so no-one is able to speak on this matter with any authority, we're all just guessing here until we get the required info.
I imagine that this is something we won't find out properly until a few weeks away from release, but as every game in a generation has been compatible to date, I'm sure GameFreak are going to ensure that Gen 6 is no different and my personal opinion is that they'll use the more sophisticated tech of the 3DS to patch the game.