First of all, adding new Mega Pokémon won't cause trouble with X and Y because Nintendo/Game Freak can just add the data for those to X and Y with a mandatory patch. They've done it before, they can do it again.
Obviously, Mega Latias and Mega Latios will be made available in OR/AS. Mega Kyogre and Mega Groudon are also far from unreasonable. Because Rayquaza is supposed to be able to beat Kyogre and Groudon at all times (in the lore at least), I can see a Mega Rayquaza happening too.
Mega Blaziken is already a thing, but the Blazikenite can't be obtained any more now that the wifi event is over. I believe that Blazikenite will be made available to everyone once again in OR/AS, along with Sceptilite and Swampertite. Mega Sceptile and Mega Swampert are happening.
Now, let's look at what NPC's used Mega Pokémon in X and Y. The Champion and the leader of the evil team. If OR/AS are truly Ruby and Sapphire remakes, the Champion will either be Steven or Wallace, and the evil team leaders are Archie and Maxie. And what are the main Pokémon of these four characters? Metagross, Milotic, Camerupt and Sharpedo. Mega Metagross makes sense because other pseudo-legendaries have received Mega Evolutions. Mega Milotic would be a good counterpart to Mega Gyarados. And Camerupt and Sharpedo are each other's counterparts.
TL:DR: Mega Sceptile Mega Swampert Mega Camerupt Mega Sharpedo Mega Milotic Mega Metagross Mega Latias Mega Latios Mega Kyogre Mega Groudon Mega Rayquaza
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