"I am Mewtwo, the world's most powerful Pokémon." –Mewtwo
I hope this quote inspired you to give your Mewtwo a great moveset as much as it did me.
Okay, so I have 3 seperate movesets: two for each Mega Evo and one if you're playing in Gen 5 or earlier.
Mega Mewtwo X
@ Mewtwonite X
EVs: 252 Atk / 252 Spd / 4 HP
The first two are STAB moves that have good coverage by themselves. Earthquake has great power and coverage, and Poison Jab just became great for killing Fairies.
Mega Mewtwo Y
@ Mewtwonite Y
EVs: 252 Sp. Atk / 160 Spd / 100 HP
Psystrike is a STAB move that does physical damage (nice since Pokémon that are weak to Psychic often have good Sp. Defense). Aura Sphere is good for Dark-types, as well as many others. And of course, Mewtwo gets the BoltBeam combo.
@ Expert Belt
EVs: 252 Sp. Atk / 252 Spd / 4 HP
Since both Mewtwo and Mega Mewtwo Y are special attackers, they have the same moveset. Note that the held item and EVs are different, though.
So there you go. Mewtwo is a great competitive Pokémon, as its Mega form is the most powerful
in the entire game. I hope you liked it, and if you did or have anything to say, feel free to leave a vote/comment.