That's what I'm expecting too! I think, if we do get the Emerald storyline in the games to go like this:
1) In OR, you fight Magma, in AS, Aqua. The team not corresponding to your version is your ally.
2) Here's the twist: In your respective versions, your corresponding team awakens their corresponding legendary... but so does the other with their respective legendary!
3) Then, it's classic. You have to call Rayquaza to stop the two from fighting ala Emerald. Here's another twist: Only one legend leaves the battlefield( the legend that's not corresponding to your version) while the other remains to challenge you. It's your typical legendary battle.
4) Post game, there 'll be an arc concerning the other team who's looking for the other legendary. Your team tries to stop them, and it all ends in a battle with that legend too!
5) Should you catch the two, you can then battle Rayquaza at Sky Pillar.
What do you think?