That implication came to me too. It seems like that may be the case or they'll have to recon the Mega evolutions to fit with the real evolutions if they were to ever give them any in future generations...
So with that in mind I'm hoping third stage Pokémon are the one's that mostly get them.
Now with Mega evolutions they could use this to give the Hoenn mascots Mega evolutions for the remakes and put them in the cover to attract attention...sort of like how Giratina forme made people buy Platinum Version and lesser so (due to being a sequel and not a third version/ remake of an old game) Kyurem formes made people buy Black 2 and White 2 versions.
Though there will likely be remakes, who's to say they'll occur in Gen VI?
I think they still need to do Third-Game remakes first, Yellow and Crystal, before moving on to R/S/E
That is a good though. Maybe X and Y will have some, but not all Mega Evolutions, and the Sequel(s) will have Mega-Evolutions for bigger names. The first two will have mostly normal pokemon, and the Next will have Legendaries, to make people want to get it(them). [Leaning more towards it, Because Pokemon Zed (i think it should be Zed not just Z because zed is cooler)] And since Legendaires,for the most part, are much more limited in number, it'd fit well.
On that note, a sort of, alternate version of my Single-Pokemon theory. Maybe it will work for any pokemon of the species, BUT, like the DNA Splicers, it can only work for one, at a time, for each species that has it. And again, depending on if it's a hold-item induced evolution, which I'm assuming it is, it'll function like Battle Facility ruling, only one per team. [Of course not a lot of people have teams of multiple of the same pokemon.] Maybe you give the stone to one Lucario, and, like the DNA splicers saying they don't work on another kyurem, the Bag won't let you give it to another Lucario. Or if you can, it just won't trigger. X and Y already seem to have much more complex coding, so this isn't too far out of possibility.
As a repeat to things mentioned above, one, SUPER POKEMON, [let's just hope it doesnt take five rounds/episodes :P]
I do like the name Awakened forme....sounds much cooler.
And the Ability concept...now that makes a lot of sense. Each pokemon could be given a new hidden ability, [different from the ones they already have] and only with THAT ability, will they trigger mega stones. Then they wouldn't have to be event exclusive, but still be quite rare. They could slide them into the Dream World, or Dream Radar [if they make a new version/update the current one for X and Y] and maybe have in-game trades/gift pokemon with the right ability. [Maybe for achievements, like HG/SS getting the other Starters for completing the Pokedex]