Okay, I just thought of something. What if these crystals could actually somehow be used in conjunction with Mega Stones? You could use them to charge a mega stone with either Light/Solar or Dark/Lunar energy to achieve Light and Dark mega forms.
Okay, the evidence for this theory is a bit shaky, but here goes.
I'm thinking that the Mega Charizard X and Y split could actually be a preview of this principle, with Charizardite X and Y just being two instances of the same mineral after being charged with two different types of energy. That sounds pretty improbable, but just compare the two designs and hear me out.
Notice the differences between the two designs. Charizard Y has a gallant, confident pose and retains his original, bright color scheme and orange fire (you know, same color as the Sun) along with having wrist blades that are actually kind of like those possessed by Gallade.
Charizard X, on the other hand, has a much more menacing posture, with its hands half-clenched, its eyes red with anger and supernatural fire billowing out of its mouth as though it can barely even contain its rage within its body. It has a black and blue color scheme (the two colors most often associated with night) and a ton of spikes on its body.
It's possible that in Sun and Moon you'll be able to choose which mega form you want, whenever you want, by charging it with the sun or moon stone. Or maybe you'll only get the sun OR moon stone depending on which game you buy, and you'll be able to trade your charged Mega Stones back and forth.
Another quite arbitrary reason is the leaked Mega Milotic in Tyranitartube's Alpha Sapphire randomizer playthrough, which I'm...about 75% sure is legit but I haven't actually managed to find anything that positively confirms or debunks it.
Either way, two things about it:
1) I'm pretty hopeful that Sun and Moon will introduce Mega Milotic since it's supposedly going to take place in Hawaii, which is full of all kinds of colorful tropical fish in real life, and Milotic is one of the more popular fish Pokémon.
2) Something about this design just strikes me as not very...Milotic. I mean, making it red, giving it horns and all sorts of weird black and white markings...more like Darth MAULotic, amirite? it just doesn't seem like something that a Pokémon that stops wars just by sticking its face in your field of view would turn into. ...You know, unless it was somehow charged with a great deal of dark energy from the moon or something crazy like that.