I don't think so, for several reasons.
1. Perfect Zygarde does not resemble Z anymore.
Instead it now has more features that are reminiscent of Xerneas and Yveltal, particularly the X and Y-shape aspects. It has 4 spikes on it's "crown" and 4 X-symmetrical "shoulder-wings", but these wings are also flat and elongated like Yveltals, while also having a 5th one as a tail, which along with the wings coming out sideways form its shoulders combines makes a Y. The Z-shape we saw in its serpentine 50% forme is practically gone.
So this makes at least the point, that if there is to be a single version, it would much likelier be called Pokemon XYZ or even Pokemon XY2, rather than Pokemon Z.
2. Thousand Waves / Thousand Arrows
As before, there is still 2 counterpart moves that are Variations of Land's Wrath. Them being Variations implies that they would replace Land's Wrath one at a time (even moreso than Ice Burn/Freeze Shock replacing Glaciate), rather than learning them in addition to it (it would have 3 moves that are all Land's Wrath in terms of type, power, accuracy, targets, being physical, PP, just with different added effect).
|Land's Wrath, an inferior version of Thousand Arrows/Waves|
It could of course also be that the canine 10% Zygarde-form gets the Waves one while the perfect one gets the Arrows. But Waves is still superior to Land's Wrath, so it would be strange for the inferior form to learn it. Usually in Pokemon, inferior forms either learn the identical signature move, or lack just that in their learnset (Phione not learning Tail Glow and Heart Swap for example despite it's learnset being identical to Manaphys otherwise).
3. 6 game-origin markers for Pentagon-symbol
Long ago, while researching the game-data of XY, the guys at projectpokemon found that there is a special marker that each Pokemon can have, which is determined by the version the pokemon is encountered in and then causes the blue pentagon-symbol to show up in the status screen (also known as "Kalos-born"-symbol from before ORAS). So X uses a different value than Y, and if you look at the data of a Pokemon with the pentagon-symbol, you can tell what version it is from. They also found that there is a total of 6 different values that cause the pentagon-symbol. X and Y were the first two of course. When ORAS came out, it was confirmed that OR and AS use 2 more of those values... which leaves another 2 markers for generation 6. And that would make perfect sense if they intended to have 2 XY-sequel versions as the final games this generation.
4. 2 Versions automatically sell more than one
If Gamefreak finds even the slightest "reason" to do 2 versions, they will.
But the question remains. Given that Perfect Zygarde already embodies both Life (blue/Xerneas) and Death (red/Yveltal), what could possibly be on 2 box covers then?
Here are some possibilities:
- A second set of forms for Zygarde.
One part that seems imperfect about Perfect Zygarde to me, is that its design is dominated by black. Especially since the serpentine forme seemed to be quite equally and asymmetrically balanced between black and green. So what if there was a second set of forms? With the other perfect Zygarde also having red AND blue marks, but being a very different design and dominated by green colour?
There is even precedent for something like this happening. Mega Mewtwo. We were shown Mewtwos Mega evolution, we saw it battle Genesect in a Pokemon movie, and it was only almost a year later that we found out, that there is actually two Mega Mewtwos and the one we knew was just Mega Mewtwo Y.
Perhaps Perfect Zygarde 1 will be featured in the Mega special Act 4, but the movie will focus on the hypothetical other Perfect Zygarde we haven't seen yet.
- Even stronger than "perfect", version exclusive Zygarde forms.
A bit of a stretch considering that the one we know is already flat out called perfect.
- Intermediary "75%" stages between the 50% and the Perfect form.
This one is more realistic than the previous, because the known Perfect one would then be the ultimate one that you need an Item or other trigger from both games brought into one.
Kind of like, if instead of there not being an "original Dragon" at all in gen V, but were shown the "original Dragon" first and then got BW2 with Black/White Kyurem on the cover. Doing properly with Zygarde what they didn't with Kyurem.
- Mega/Primal Xerneas and Yveltal.
Still entirely possible that they would get some kind of new forms too, which would explain why Zygarde suddenly gets activated when it didn't the last time.
- some new form for AZ-Floette
That would cetrainly be unexpected, since it is already a special NPC-related variation of a Pokemon that is not even fully evolved, but who knows what Gamefreak could have planned for it that we would never see coming.
I would not have included this point if it wasn't for the Pokemon Marketing Director having said that "Flowers" are the near future of Pokemon.
Also, for some reason, the shiny form of Zygarde has the same colour palette as Florges. Coincidence or could this possibly somehow become relevant? Probably not..
AZs Floette is definitely going to play a role in the next game though, regardless of who makes it on the covers.
- An ORAS-sequel with a new Primal mascot.
Yeah.. I've fallen very low at this point.
But let's entertain the idea anyway. Generation 6 so far, has had 2 pairs of games. Each time red and blue. The logical completion of this set would be a pair of green games, each being a sequel to each pair.
It's also certainly not coincidence that both XY and ORAS feature mascots that threaten to cause huge imbalance to the ecosystem. And in both regions, there is a third legendary, which is green, is primarily a Dragon type, but having opposite secondary types of Flying and Ground.
Obviously if the "other green game" was a third Hoenn game centered around Rayquaza, it would not be an Emerald remake, it would have to be an actual sequel. And it also would not have Mega Rayquaza on the cover, but some new form for it instead, which would be even more powerful.
A primal Rayquaza? a Perfect Rayquaza? A Rayquaza that has Alpha and Omega symbols on it's body? A Primal Regigigas?? Yeah, told you this one was shaky.
As ridiculous as it sounds, right now is actually the only situation when it would be profitable for Gamefreak to release 2 completely different games simultaneously. Why?
Because both projects would be sequels, meaning neither had to be made from scratch (one is an altered XY-game the other an altered ORAS-game), so just a few places changed and added, and a new story thrown into the already existing regions.
But while they would be the most diverse pair of games so far, they would still both share many of the new features that would be added, so it's not like they would have to be handled like 2 completely different products.
They'd both get the Maison replaced by a full-blown long-awaited and teased at Battle Frontier. They'd both include the same third wave of new Mega evolutions. And they would both have featrues cross-over that players missed out on (Soaring and Contests in Kalos, Boutiques & Trainer customization in Hoenn). And the plots and characters could of course cross-over between the regions.
This is the least realistic possibility of all of these of course.