So the problem I see with Mega Mewtwo Y is that it is more susceptible to revenge killing from the likes of the Ekiller and Giratina-O (not to mention Aegislash), while Modest Mega Mewtwo Y is still outsped by Timid Darkrai (which is going to be a threat this generation, given Dark's improved coverage).
Mega Mewtwo X gains STAB on Aura Sphere but loses Life Orb boosts, so it has a much weaker Psystrike.
I've been running regular LO Mewtwo on Showdown with decent results, a moveset of Psystrike/Aura Sphere/Ice Beam/Flamethrower still does an asston of damage (if you can attack as it Geomances Psystrike does 60%+ to the 144/0 Xerneas, bringing it down to the killing range of an unboosted Extremespeed or Shadow Sneak).
Mega Mewtwo X gains STAB on Aura Sphere but loses Life Orb boosts, so it has a much weaker Psystrike.
I've been running regular LO Mewtwo on Showdown with decent results, a moveset of Psystrike/Aura Sphere/Ice Beam/Flamethrower still does an asston of damage (if you can attack as it Geomances Psystrike does 60%+ to the 144/0 Xerneas, bringing it down to the killing range of an unboosted Extremespeed or Shadow Sneak).