I find new Mega Evolutions pretty unlikely, and that's because ORAS still need to battle with XY.
In previous games, when new forms were introduced mid-generation, when battling between, say, the other player's game would display it as its original form, but with the stats, moves, (and if applicable, type) of the new form.
However, Mega Evolution occurs during battle. I can't imagine how they'd get XY to recognize an in-battle mega evolution that, as far as XY is concerned, can't happen.
The closest thing I can think of is Giratina's Griseous Orb, which in Platinum, will always be moved to the Bag if you attempt to trade it. They could do something like, if you are facing an X or Y game, the Mega Stone is moved to the Bag.
But, that has its own problems. If you're intending to use a Mega Evolution, the moveset you choose is likely going to be far more suited to that Mega Evolution. By simply taking it out of the bag without asking, you hurt your team, because that Pokemon is less able to do the job you trained it for, and, also, have no opportunity to replace it with a different held item that might be useful.
Edit: For the record, this is not about the Eon duo. This is referring to the Mega Sceptile, Swampert, and Weather Trio people have been talking about.
