Well, I was under the assumption that the Pokédex is something given from a Professor to a young trainer they can trust to gather data on what's available in the region. I don't believe everyone has one but considering the National Dex is an upgrade, I'd assume that the Pokémon Professors would know about the prior data (and be retconned to know of even more as in the case of FRLG/HGSS) of other regions. Unless the Pokémon Professors are a bunch of uneducated hacks.
I do believe that someone encountered those Pokémon even if they canonically weren't caught.
You make a good point. It's late, so I'm not at my sharpest right now, but it is indeed entirely possible that Red and/or Ethan/Lyra encountered Mewtwo, but failed to capture it (in fact, as you suggested, that could be what drove Mewtwo out of Cerulean Cave and caused it to relocate to Kalos). If that were the case, then there
would be Dex data on Mewtwo, albeit incomplete data. But still, it would be enough to make its existence known, and then Professor Oak/Elm would probably publish a paper on it or something in order to share that data with the scientific community.
That's a good solid theory. But, considering Mewtwo's genetic code is already tampered with, who's to say Mewtwo's tampered DNA isn't why it reacts to the stone?
Hmm. Well, that's certainly a possibility. Actually, we don't even know for sure that
any Pokémon's genetic code is what the Mega Stones react to. I just assumed that to be the case because it seemed the most likely, and if some scientist wanted to create the most powerful Pokémon there could be and decided to give it the ability to Mega Evolve, I imagine that they would try to find whatever it is that keys in the Mega Stones to a particular species of Pokémon and then modify one in order to match their creation.
The device itself is manufactured but it requires the key stone in order to trigger it. To me, the device is nothing more than a holder/fashion statement. Think of it like a cellphone clip, is the clip what allows you to text/make calls or is it the phone it holds?
That's what I thought at first, but Gurkinn says in XY that he only has one Mega Ring at the time of your's and Serena's challenge. If it were just a "clip," then his lack of another Mega Ring would be irrelevant and he would just need to give you the Key Stone (which, oddly enough, is mentioned only once over the course of the entire story, and not even by name). Furthermore, the item description of the Mega Ring states that it contains an "untold power" that enables a Pokémon to Mega Evolve, and it is shown in the post-game that the Mega Ring is capable of being upgraded when the player comes into contact with the Anistar Sundial after being exposed to the energies of Xerneas/Yveltal in Team Flare's headquarters. So evidently the Mega Ring is far more than just a container for the Key Stone and is likewise a crucial element of the equation.
That being said, however, it does seem as though whoever is manufacturing them is doing so without fully understanding what it is that makes them tick. Or perhaps the pioneer of Mega Evolution was the one who originally devised the design of the Mega Ring and recorded it in a journal or something.
Simple: X & Y are essentially two different timelines with the same situation that can "cross-over" with each other (which was something I thought about all prior paired versions but was sorta confirmed by the messages at Lumiose City). So the legendary acting as a battery for the weapon in the respective version are what power up the stones and the stone is what makes the specific Pokémon react. Most of them are the same between the two legendarys, but for Charizard and Mewtwo the Life/Death power of the stone affects them differently. So bringing a Charizardite Y into X doesn't turn it into a Charizardite X, it remains powered by Yveltal from the Y reality and thus allows it to transform into Mega Charizard Y even in X.
Even simpler: The pokémon with branched Megas react to the stone that was changed and charged by a specific legendary, so their formes are a reaction of that.
It would also sort of explain why Mega Houndoom reacts only to a stone infused with Death...
Ah, yes, of course. I completely forgot that the Mewtwonites/Charizardites are version-exclusive. That would explain why Charizardite Y Stones don't exist in the X timeline; the stones that became Charizardites were never exposed to Yveltal's energies at all.