Unsolved Mysteries in X/Y...

[Ziggy Stardust]

I find it odd that mega evolution and stones existed in ancient times but MewTwo, a man-made Pokemon from the present, has a stone dedicated to it. Unless someone--likely Team Flare--has found a way to produce them.

What came first, the chicken or the egg?
Perhaps the stone was produced before Mewtwo was created and had no known use before then.
Maybe there's still Mega stones in the Pokemon world that don't work on any present known/existing Pokemon.

There are some theories. One says Mr. Fuji actually managed to create artificial Mega Stones. Two for Mewtwo...

Spoiler

... and one extra for Charizard.

And that would be why Mewtwo and Charizard have two Mega evolutions. These are artificial.

 

[Absent]

^Crossing canons to form a theory, careful there.
I like the theory that somehow Mewtwo's stone got radiated by the Ultimate Weapon and turned into a Mega Stone.

 

[Champion Red]

That's actually a good idea. Maybe somehow the Ultimate Weapon effected Mew's mega stone, and warped it into Mega Mewtwo Y? Then X was created through experimentation by Team Rocket/Flare/Fuji