The end of the Groudon/Kyogre conflict has us being told that new Pokemon are reacting to Mega Stones and then we start getting Mega Stones appearing in locations we've already been (like next to Birch's lab for Mewtwo X). Seems like a heavy implication that the energy created new stones too.
So I didn't just imagine that Mega Stone next to his lab being there all of a sudden...
I know that Birch said that the resolution of the crisis caused Pokémon that used to live in the Hoenn region thousands of years ago to return, but I don't remember him saying anything about Mega Stones. Maybe I missed that?
Nothing said that the stones that are changed only affect Pokemon of the same type or anything. The energy alters the stone to do something it shouldn't be capable of doing in the first place, so I don't see why other changes couldn't be made during that process.
Indeed. Technically, it's only speculation on Sycamore's part that the stones that were mutated were Evolutionary Stones specifically, but then, they were irradiated with a cocktail of various energies, so I don't think it's too much of a stretch to think that they were altered on such a level so as to go further outside of their boundaries than normal, especially when, as you say, they aren't even supposed to trigger Mega Evolution in the first place.
The only mega stone's origin we know for sure is Rayquaza's (the meteorite).
Everything else is just speculation, but we do know that some of them are related to Z's weapon and Anistar City's big crystalline sundial.
Speculation, yes, but very well-evidenced speculation still. Sycamore's theory about the Stones being created by the ultimate weapon was shown to be at least mostly correct when he had you touch the Anistar Sundial in order to upgrade your Mega Ring, as he was operating on the logic that you, too, had been irradiated by the same energies on some level when you made contact with Xerneas/Yveltal in Team Flare's HQ. And then there's the fact that this universe, which
did see the occurrence of AZ's war and the creation of the ultimate weapon, which supposedly created the Mega Stones, has Mega Evolution, whereas the old universe, which had no war and no weapon, does not. So the weapon has to be at least mostly responsible for the emergence Mega Evolution, because if there are any other significant sources, then surely, in the old universe, they would have been discovered?
Oh yeah, the Key Stones' energy was what I remembered that was related to humans. I might be just dense, but honestly the science behind this makes very little sense. To be fair it is Pokemon, but it doesn't seem like they put in much effort to make it logical, just to connect it to X/Y and Mega Evolution lol
The only thing that I'm not clear on is how Key Stones contain human energy, although I have a theory (that they don't
naturally contain human life energy, but rather, they
transmit it). But as far as Pokémon being used as an energy source, I think it makes perfect sense. Just think about Pokémon in general, and about how they can seemingly create and gain mass from nothing. Where does the energy for things their attacks or evolutions come from? We've known since at least Gen IV that Pokémon let off energy when they evolve, and Team Galactic was even said to have been researching ways of harnessing that energy for other purposes. Of course, they were only just beginning to break new ground with that thinking in that universe, as there was never an ultimate weapon in that version of history. In the new timeline, the idea that Pokémon life energy can be harnessed in order to power technology has a 3,000 year precedent.
Anyway, my point is, now we have something of an answer that elaborates on the otherwise-nonsensical abilities of Pokémon to create mass out of seemingly nowhere. It actually comes from the Pokémon themselves, which are in fact major energy sources.
Mega Evolution takes the principle of regular evolution and the energy that the Pokémon let off when that occurs, to an even higher level by boosting it with human energy transmitted through Key Stones. More energy = further evolution.
Honesty, I find it rather amazing as to how well this all holds up, despite obviously not being planned very far in advance.