Just like few of the members here have said, the best / easiest way to crush M Mewtwo EX decks is with the new M Gardevoir EX (STS). The 2 energy Despair Ray attack OHKO's him.
This past weekend I went to a LC and out of 5 rounds I faced 3 M Mewtwo Decks. Deck 1 and 3 I had problems setting my M Gardevoir EX's faster than he could set his M Mewtwo EX's. But once I had one M Gardevoir EX out it was game. For the match up against Deck 3, I was able to stall a little bit with Giratina.
With the second M Mewtwo EX deck I faced, I won in 3 turns thanks to a perfect opening hand.
2x Gardevoir EX
1x Fairy Energy
1x Spirit Link
1x Fairy Garden
1x Shaymin
1x Sycamore