Mega Mewtwo X
Pros:
- Pretty good offensive typing, with two STABs and its fighting type covers a psychic type's weakness
- Great attack stat and good speed, capable of being a very formidable physical sweeper
- Access to Earthquake, a powerful physical coverage option
- Can utilize Drain Punch for significant HP gain to compliment decent bulk
Cons:
- Lacks a strong psychic type physical move, and is limited to Psycho Cut and Zen Headbutt
- Lacks stronger fighting type physical moves such as Close Combat and High Jump Kick, and Low Kick can be situational
- Physical elemental coverage moves such as Fire Punch are much less powerful than special ones like Fire Blast
Mega Mewtwo Y
Pros:
- Great special attack stat, also making it an offensive threat
- 10 stats faster than Mewtwo X, oustpeeding Mega Gengar, which is a powerful threat
- Thanks to better special attack stat, Mega Mewtwo Y is great with Psystrike, a powerful and accurate STAB psychic move that breaks special walls like Ho-oh, Blissey, and Chansey
- Great coverage options such as Shadow Ball, Aura Sphere, Fire Blast, and Ice Beam
- Access to Calm Mind, a great set up move that is complimented by exceptional special defense
Cons:
- Is very weak against Sucker Punch, which is commonly run on Yveltal
- Has only one STAB, slightly hindering offensive capabilities
Who is better?
Mega Mewtwo Y is the better mega in this case. It is faster and Mewtwo's special movepool is much better than physical, consisting of a powerful STAB Psystrike and more powerful coverage. Mega Mewtwo Y is probably weak against Yveltal, which is very common, but Mega Mewtwo Y's advantages outweigh the disadvantages.