X and Y also reference past games, like mentioning Team Plasma. I assumed the multiverse thing was to mainly either explain why megas and fairies weren't in the past games or to allow people to build their own idea of which versions are "canon." For instance, if you played White over Black, then you could say that was canon. Though, B/W is not the best example since it also teased both being canon in different timelines.
Well, the whole idea with the multiverse concept was that the two universes were practically identical aside from a few key differences. AZ's war, Mega Evolution, Fairy types, Mewtwo being in Kalos instead of Kanto, the Sea Mauville replacing the Abandoned Ship, Archie/Maxie not failing their science classes on every conceivable level, Hoenn in the 3DS Universe being more technologically advanced than in the GBA/DS Universe, and so on and so forth are key differences, but by and large, everything still happens the same way - we still have Team Aqua and Team Magma in Hoenn led by Archie and Maxie, Roxanne-Wallace are still Gym Leaders, Steven is still the Champion, his dad is still the president of Devon, Brendan/May still become the Champion, May/Brendan and Wally are still their rivals, etc.. So when XY talks about Team Plasma "making news in the Unova region a while back" (which is all that it says), it's just talking about this universe's iteration of Team Plasma. We don't know what they did that made the news or even if their goals are exactly the same in this universe, but we know that they exist, which stands to reason because there isn't really that much of a variation between the specific individuals who live in either universe or what they amounted to in their lives (indeed, a major point of Zinnia's character is that wishes to meet her departed comrade Aster once again, and it is implied that she wishes to find Aster's GBA/DS Universe counterpart).
Not so sure this is the case; references are made throughout XY to earlier games. I believe it would go original timeline (no Mega Evos, so no Draconids and Kalos possibly being destroyed in war along with AZ (Ancient Ruins such as Relic areas could be outposts of Kalos but be extremely old now, obviously)). So FRLG/ RSE (~same time) - HGSS/DPPt (~same time) - BW - BW2, and this alternate, Mega Evo timeline would be pretty much the same, just XY/ORAS (as far as we know around the same time) after these, or, very confusingly, it could be:
ORAS
Emerald (?) (included due to Emerald references being more sequel-istic than third version)
XY (or vice versa, honestly, who knows?)
Same thing as I was saying. In a situation like this, they're not technically references to past games - in a meta sense, sure, they are, but story-wise, they're just proof that this universe contains its own versions of people and events that also exist and did similar things in the other universe, and we don't even have to look any further than the plot of ORAS in order to see that that is true.
Zinnia specifically says that the other universe is less technologically advanced, and that it never featured AZ's war or Mega Evolution. However, we know from playing those games that the general "shape" of that universe is the same as this one. Events unfold in essentially the same way, except for a few key differences where they apply - the absence of Mega Evolution and AZ's war shouldn't stop Team Plasma from existing, because they formed independently of any of that stuff. However, the plot of XY simply
cannot happen in the GBA/DS Universe, because it is so heavily predicated upon Mega Evolution and AZ's war. But there's still a Kanto, there are still those same Gym Leaders, and so on. So the universes are structured as such:
(GB/GBC Universe: RGB > GSC)
GBA/DS Universe: FRLG/Emerald > HGSS/Platinum > BW > B2W2
3DS Universe: ORAS > XY
Not trying to be rude, but it seems as though people aren't seeing the bigger picture here.