If an XY and an ORAS player try to trade with each other, and the XY player scrolls through the PC of the other, he might notice fully trained Groudon and Kyogre with only three moves, or 'mons like Gallade or Sharpedo holding no item. And error messages aplenty if he tries to trade. Game Freak has made some strictly incompatible stuff in Gen VI in ways it never did before. Forme changes in earlier generations required overworld interaction or Key Items, not items like Mega Stones that should be visible in the trade interface. ORAS was also the first time completely new moves were introduced mid-generation, breaking trade compatibility completely with their preceding games, and also quite a few previously-thought-unassailable conventions. Coincidentally, my strong conviction that this would be impossible, and willingness to take on embarrassing bets over it, is the reason why my nick is not Cobraroll any more.It would still probably upset a lot of Pokemon fans though, so I don't see them doing it. I feel like there would be backlash, and they haven't done such a thing before.
That being said... entirely new Pokémon is a whole new ballpark, and they've opened a bag of Alola forms already, so my guess is that they'll just stick to the policy of adding new forms, not new dex numbers. Then again, there is no National Dex in Sun and Moon, so... this gen, I'm not taking any bets.