As much as I hate the idea of third versions coming back, I have to admit I can see it happen with X&Y because of their story. It goes without saying, this is all speculation on my part.
Let's see. Gen 1 and 2 didn't have any differences in stories between versions (being able to catch Ho-Oh first and Lugia later and vice-versa doesn't count, they weren't an actual part of the plot) , so third versions could easily be made without altering much of the plot.
Now, starting from Gen 3, version mascots became an integral part of the story, and third versions were scripted with one rule in mind: to not make one version of the original pair look closer to the official canon than the other, if you know what I mean. So:
- In Ruby, Team Magma learns about Groudon and tries to wake it up; Team Aqua, assisted by the player, tries to stop them before they do. Kyogre is completely absent from the plot.
- In Sapphire, Team Aqua learns about Kyogre and tries to wake it up; Team Magma, assisted by the player, tries to stop them before they do. Groudon is completely absent from the plot.
- In Emerald, both teams learn about their respective Pokémon, each team tries to wake up its Pokémon before the other team does. The player has to stop them both.
And ditto for Gen 4:
- In Diamond, Cyrus plans on using Dialga to remake the world. Palkia is only mentioned, but otherwise absent.
- In Pearl, Cyrus plans on using Palkia to remake the world. Dialga is only mentioned, but otherwise absent.
- In Platinum, Cyrus plans on using both Dialga and Palkia to remake the world.
But come Gen 5, and... we have a problem: the entire plot revolves around the player having one of Reshiram/Zekrom and N having the other! There was no way to combine both stories into one, without discrediting either the Black version or the White version, and maintaining the Black VS White theme (so, no Kyurem VS Reshiram and Zekrom) . But since GF wanted to still make something in Gen 5, they made sequels.
Gen 6 went back to a more basic story where, again, the version mascot is used by the main villain, and its counterpart is a no-show, just like in Gen 4, so both versions of the story become once again easy to combine into one. This is what I can see happen in Gen 6 (spoiler tag just in case) :