Okay, there's some things I'd like to point out.
First of all, Junichi Masuda has already ruled out the possibility of sequels to X/Y, by saying: "Instead of doing a direct sequel to X/Y we're tying it together in some unique ways."
This means that we're not getting a direct sequel to X and Y. And looking at the two unused moves in the game, as well as the two placeholders in Pokémon Omega Ruby and Alpha Sapphire's coding definitely confirms that there will be two games released this year. Not just one, but two.
So what could this mean, hm? Well there's three different possibilities:
1. A prequel to Pokémon X and Pokémon Y in which is set in Kalos 2 years before the events in Pokémon X and Pokémon Y. Possible names: "Pokémon X Zero and Pokémon Y Zero", "Pokémon New X and Pokémon New Y", "Pokémon ZX and Pokémon ZY".
2. An upgrade of Pokémon X and Pokémon Y, set in the same time as Pokémon X and Pokémon Y. Possible names: "Pokémon ZX and Pokémon ZY".
3. A remake of either Generation I or Generation II, with Zygarde as the main legendary. Possible names: "Pokémon Zygarde Red and Pokémon Zygarde Green", "Pokémon Zygarde Red and Pokémon Zygarde Blue", "Pokémon Zygarde Gold and Pokémon Zygarde Silver".
4. Set in a new region, with all the same Pokémon as in Generation VI, but with an entirely new storyline. Possible names: "Pokémon Arrow and Pokémon Wave", "Pokémon Arrow X and Pokémon Wave Y".
It's either one of those four possibilities. But it's a high chance we'll be getting Mega Chesnaut, Mega Delphox and Mega Greninja, as the new Mega Evolutions in the games. And there's also a possibility of the Mega Evolutions of the Johto starters as well. Mega Meganium, Mega Typhlosion, Mega Fereligator X, and Mega Fereligator Y.
And as for Zygarde, it's all too obvious that it will get two new formes in the game, not Mega Evolutions. Because Mega Evolutions don't change their moves. I'd definitely speculate for a Primal Zygarde X and Primal Zygarde Y, just as Primal Groudon and Primal Kyogre had. Primal Zygarde X and Primal Zygarde Y would make more sense in this regard, since Thousand Arrows is similar to Xerneas's branch-like antlers, while Thousand Waves is similar to Yveltal's wave-like patterns. But honestly saying, it's very unlikely that there would be a fusion device, similar to what happened to Kyurem, that's why I'm saying that Primal formes are more likely, using special hold items to activate Zygarde's power. And if you think about it, Zygarde, Groudon, Kyogre and Rayquaza are the only Pokémon that were drained of their power and became weak, but we know all too well that Rayquaza only has a Mega Evolution, which then Zinnia taught Rayquaza Dragon Assent. But having said that, it could work with Mega Evolution taking place with Zygarde changing to either it's X Mega Evolution or Y Mega Evolution, then someone teaching it a new move, but that's highly unlikely though.
But that's pretty much where I say, that there is no "third version", since it won't be a standalone game, it will be two games released this year at the same time.
Also, there's a possibility that it will be enhanced for New Nintendo 3DS, but won't be exclusive. Just like how Generation V was enhanced for Nintendo DSi, but not exclusive. As such, playing on New Nintendo 3DS would improve frame rate and and allow stereoscopic 3D to be used everywhere, rather than restricted to a few areas. But playing on the original Nintendo 3DS will have slower frame rate and restricted stereoscopic 3D functionality.