there are a few possibilities that exist already. my primary suspect is guzzlord, for reasons I explained previously. I do think that Zygarde presence in the alola region is our biggest clue, which is why my secondary suspect is Necrozma. there are a few other possibilities, however I do have something to say.Before I begin, a brief shoutout to Pikachu315111 for posting something here, thus reminding me that this thread exists and that I posted here before via means of the notification system. Now, onto the actual post. I've been looking into these 3DS Pokémon games extensively since my last post here, and while I definitely think there were some significant changes made to the core series lineup here, I also have reason to believe there was some scrapped content, too- some of which, dare I say it, we might actually see in Pokémon Legends: Z-A. I'm going to keep the theorycrafting and whatnot to a minimum here- that is to say, there won't be any- but I would like to bring some attention to the Hoenn remakes to try and tie up some of Kalos's own loose ends.
Something that's always fascinated me is how "remake generations", a term I use to categorize generations that, well, have games that are remakes, tend to share a ton of similarities with the generation that is being remade. Sure enough, Gen 3 (Hoenn) and Gen 6 (Kalos) seem to have a lot of smaller details in common. Among these, the mascot Legendaries stand out, not just because we know X & Y's story was originally going to be followed up on, but also in the sense that the ORAS iteration of Hoenn treats Pokémon Emerald differently than the RS version. I don't think the Battle Frontier's exclusion was meant to be a deliberate troll at all. If anything, this and the scene where Steven tells Wallace he wants to travel in the postgame after the Delta Episode seems to indicate that, at least in Gen 6, "Pokémon Delta Emerald" could have actually been a true ORAS sequel instead of "just an Emerald remake". The only difference would have been it would only be one version unlike how Black 2 & White 2 (and possibly USUM) handled things. The question remains, though- what does Kalos have to do with any of what I just said, especially when, unlike a Kalos follow-up, Delta Emerald was seemingly never in consideration from the start?
Remember Xerneas and Yveltal? More specifically, their Abilities? Unlike the mascot legendary pairs from Gens 2, 4, and 5 (as well as 7, 8's Crowned Formes, and 9), the Gen 3 and Gen 6 pairs not only have different typings, but also contrasting ideas on the same Type of Ability. Notice how Fairy Aura and Dark Aura can be seen as a parallel to Drizzle/Primordial Sea and Drought/Desolate Land, as well as how Aura Break and Air Lock/Delta Stream both serve as "counters" to each of their first two. That's great and all, but now shift your focus to Rayquaza's appearances across Gen 3, and again in the Delta Episode in Gen 6. Any Gen 3 fan worth their salt can tell you about the iconic rivalry between Rayquaza and Deoxys that's been a staple for both of those Pokémon's lores since 2004.
You can probably see where this is going: if the Kalos and Hoenn mascot Legendaries have all these similarities... where is Zygarde's own Deoxys equivalent? As it turns out, we may have already had our answer, long before Pokémon Legends: Arceus, let alone Z-A, was even conceptualized. On the website The Cutting Room Floor, users of that site have documented a strange gap in the National PokéDex numbers for different Kalos Pokémon. Pokémon have their PokéDex numbers changed during development all the time, but this particular gap feels almost deliberate. During development, internal index numbers are used to sort Pokémon before their PokéDex numbers are chosen. Index numbers 768, 769, and 770 include information for Xerneas, Yveltal, and Zygarde, while index numbers 772, 773, and 774 contain information for Diancie, Hoopa and Volcanion. So tell me, why does index number 771 contain removed information placed right in that exact spot? When you consider that the 3DS datamine leak contains two spots for Kalos follow-up games, it feels easy enough to think there could have been an X2 and a Y2 or whatever they wanted to call it. They clearly didn't go that route with Zygarde itself, though, certainly not with fusion forms with Xerneas and Yveltal. Z and A. Two versions, possibly sequels but possibly their own thing. A supposedly scrapped Legendary or Mythical Pokémon. I just feel like it all makes so much sense.
I dont think that deoxys is an important part of rayquazas lore. it was just a threat to the world that rayquaza had to deal with. no association between the two existed prior to the remakes (to my knowlege). and even if it was, rayquaza is still a part of a trio, not a quartet. I don't see deoxys as important enough to need a counterpart.