6th Gen Spoilers spoiler spoiler spoiler. Pokemon Time line

[Chaos Rush]

Pokémon XY made references to Blue and Team Plasma, and since you've used the Zelda timeline and acknowledged TP and WW taking place in the same time but in different dimensions, that means those references are only possible in the 3rd-5th Gen timeline, which according to you, the war never happened during then.

Those are some pretty bizarre jumps to conclusions there. First of all, OR/AS is established to be a separate timeline from RSE, and yet we see that both timelines are similar and contain mostly the same characters. Your logic is basically "well the Zelda timelines are vastly different, so that must mean Pokémon has to be too". And allow me to say for the third time that OR/AS outright states that the war never happened in the timeline that RSE is in.

That means the plot between ORAS and XY will be drastically different when Kanto, Johto, Sinnoh, and Unova remakes are involved, meaning no Team Plasma and such, since both plots in TP and WW are entirely different despite being in the same timeline in alternate dimensions.

That is some seriously flawed logic there. How the hell does "Team Plasma is mentioned = Team Plasma doesn't exist in other timeline". You have no evidence to back that up whatsoever, so I'll explain why that is flawed logic:

First of all, as ORAS established itself as a separate timeline from RSE, and Zinnia states that Mega Evolutions don't exist in the non-war timeline. XY's story heavily relies on the war having happened, and XY has Mega Evolutions, thus establishing that ORAS and XY are part of the same timeline (ORAS also shows the origin of the O-Powers guy and the backstory of the Battle Maison, thus further establishing that it's in the same timeline as XY).

According to your logic, just because Team Plasma and Blue are mentioned in XY that that simply must mean they don't exist in the other timeline? There is no evidence to support that (your "evidence" is freaking Zelda just because WW and TP feature vastly different outcomes) but there is plenty of evidence against that: ORAS!!! ORAS establishes that Team Magma, Team Aqua, and pretty much everything else exists in both timelines. Events are even similar in both timelines, and we can infer that Blue and Team Plasma exists in both timelines, just like Maxie, Archie, Brendan, May, Wally, Roxanne, and pretty much everyone else we've ever heard of.

As I mentioned above, ORAS went to great lengths to establishing itself as being in the same timeline as XY, and Zinnia outright states that Mega Evolution doesn't exist in the other timeline, and she also says the Kalos war never happened in the other timeline. Because the games that came before XY did not feature Mega Evolution, we can infer from this that these older (GBA and DS games) is the non-Mega, non-war timeline that Zinnia speaks of. "but XY mentioned Team Plasma!!!!" So? How the hell is that supposed to mean it's in the same timeline as the GBA-DS games? As Zinnia stated (why do you keep ignoring this fact), the Kalos war did not happen in the other timeline, and Mega Evolution does not exist in the other timeline. You keep acting as if this is some random bullcrap fact that I made up, but this is, in fact, outright stated in-game. X/Y has Mega's, and X/Y also first introduced the Kalos war, and ORAS also referenced the war as having happened in the past, and also establishes that the war did not happen in the other timeline (again, Zinnia outright states this). Thus it is literally impossible for X/Y as we know it to happen in the GBA-DS timeline where Mega Evolution doesn't exist and the war never happened. We know from ORAS's very existence as a remake that despite a major event like the Kalos war happening in one timeline and not in the other, that the events that followed centuries later are still similar. Team Magma and Team Aqua exist in both timelines, so does most people in Hoenn, and XY's mention of Team Plasma simply tells us that they caused trouble in Unova even in the Mega timeline - Ghetsis probably used a hypothetical Mega Hydreigon, and maybe his goals were slightly different too with the knowledge of Mega Evolution. I bet even in the non-war non-mega timeline, Team Flare was still causing trouble in Kalos, but they had vastly different goals since Lysandre wouldn't know of the Ultimate Weapon (since it wouldn't exist).

Also according to XY, Mega Evolutions were only said to be found in Kalos, and Fairy types were recently discovered, hinting that it's still in the 3rd-5th timeline thus explaining the Blue and Team Plasma references.

But the contradiction there is that in XY, the war happened and Mega's exist, but Zinnia says the war did not happen in the 3rd-5th timeline, and Mega's don't exist in that timeline. Also because many characters in Hoenn exist in both timelines, we can infer the same for the rest of the world, including Team Plasma and Blue. Also XY never explicitly says Mega Evolution is Kalos-exclusive, it just says the first documented Mega Evolution took place in Kalos with a Lucario (the Rayquaza Mega Evolution was not officially recorded or documented, it was an old legend. However, there's enough evidence to support that Rayquaza was indeed the first Mega Evolution, but it was not officially documented when it happened)

As for Fairy types being "new", that's really just a gameplay thing for easier explanation. In the original RS, there was a signpost on Route 104 that says double-battles were Hoenn exclusive (which as far as the audience knew, was true in 2002 when RS were the only games with double battles) but that was retconned.

I will say however though, that the whole alternate timeline things does feel like a retcon rather than something that was planned from the start of XY's development, and I'm willing to bet that they didn't come up with that idea until ORAS to explain why Mega Evolution even exists. But that doesn't change what they decided from canon though, and it's established that ORAS and XY takes place in a timeline where Mega Evolution exists and the Kalos war happened, and all games before it took place in a timeline where Mega Evolution does not exist and the Kalos war did not happen.

And as ORAS's very existence implies, events are similar between timelines, only difference is that people can use Mega Evolution in one and they can't in the other. Perhaps should more remakes come in future generations, it will establish that in the Mega timeline, Giovanni used a (hypothetical) Mega Rhyperior as opposed to a plain old Rhydon. Archer used Mega Houndoom, Cyrus used a Mega Weavile, you get the point.

(And for the hundredth time, Zinnia outright states that the war never happened in the other timeline, and you have to acknowledge that XY's story heavily relies on the war having happened)

 

[Mago Luis]

Also XY never explicitly says Mega Evolution is Kalos-exclusive, it just says the first documented Mega Evolution took place in Kalos with a Lucario (the Rayquaza Mega Evolution was not officially recorded or documented, it was an old legend. However, there's enough evidence to support that Rayquaza was indeed the first Mega Evolution, but it was not officially documented when it happened)

Well, there is this dialogue with Prefessor Sycamore and Diantha, which happens when the player enters the monorail station in Coumarine city:

Professor Sycamore: And why are there examples of Mega Evolution only in the Kalos region? There's still so much we don't know...
Diantha: Does this make you think of something like Kalos's Legendary Pokémon?
Found only here in the Kalos region, right? Nowhere else? Maybe that's not a coincidence.

I think this is the only time that Mega Evolution is said to be exclusive to Kalos, but it is said by the professor who is researching it and supported by the champion who wields it.

But of course, looking at the lore ORAS introduced, it really seems like the above conversation shouldn't happen. Especially because of this:

Professor Cozmo: A relationship between the Mega Stones, Key Stones, and the Meteorites...
My, but new facts do come to light every day! This is what makes my research feel worthwhile!
I know a man, a dear friend in the Kalos region, who has been researching Mega Evolution.
We worked together a few years back here at Meteor Falls researching Meteorites.
I'll have to share this information with him at once.
It might propel his research forward, and help future Trainers and Pokémon. I hope it does.

I'm not sure when that dialogue becomes available, but it may be after the Delta Episode. That's the point I'm at, and he says that whenever I talk to him.

Anyway, there may be branches in the timeline after the "main" Mega and non-Mega split. So ORAS could be in a different branch from XY, but still share the common past with the Kalos war and the discovery of Mega Evolution.