I think it's mostly because Mewtwo's other Mega Evolution outshines it in preview.
This is mostly because Mega Mewtwo Y's moveset is far more usable than the other variant. Mewtwo's original forme gained a lot of moves that benefitted from it's Special Attack, and not the Attack stat; Eg- Thunderbolt, Ice Beam, Flamethrower, Aura Sphere, Psystrike, Shadow Ball, Energy Ball and more.
X's type doesn't do too many favours. Bulky Psychic types resist both it's STABs, and Pokemon like Sableye (a common Will-O-Wisp Pokemon) are not affected at all. Walls like Lugia and Cresselia are prominent (the latter being less common) which make X's life unbearable. Y on the other hand, can fight back almost anything it comes face to face with (even lugia can have a tough time).
The X varaint lacks the sheer versatility the Y variant has, and although it can run a mixed set, Y can easily prove as a better sweeper. Even when confronted by special walls (bar dark types, who are usually frail and are destroyed by Aura Sphere) Mega Mewtwo Y can simply Psystrike tham away, or sometimes flat out overpower them.
Then again, X is also a common variant, you run into one in battle spot every now and then.
But I think that X is not chosen mostly because Y is usually a better option. It's not as uncommon as you think, there are many such occasions on which you'll come across one doing more work on your team than a Y variant.
Hope I helped!