I wonder if any of the XY stones besides possibly Mawile's will be in the games to begin with. Especially stones like the Kanto starters and Mewtwo's.
I think they'll likely be, or at least most of them, because Mawilite and Sablite will probably be version-exclusive. As for the Mega Stones of non-Hoenn Dex Pokemon, I could likely see them being bought at a store or given by some NPCs in the post-game.
For those wondering, these are the Megas/Primals in the Hoenn Dex:
Spoiler:
Mawile, Sableye, Gardevoir, Gallade, Alakazam, Gyarados, Pinsir, Heracross, Medicham, Aggron, Banette, Manectric, Absol, Sceptile, Blaziken, Swampert, Altaria, Salamence, Metagross, Sharpedo, Camerupt, Glalie, Latias, Latios, Kyogre, Groudon and Rayquaza.
That leaves most of the X/Y Megas as well as Audino, Slowbro, Lopunny, Steelix, Pidgeot, Beedrill and Diancie. Diancie's Mega Stone gets obtained when the event Diancie (currently ongoing in the US) gets transferred over from X/Y to OR/AS, but the rest of the Megas should probably have their Mega Stone obtainable in the post-game.