Hello there well i like mewtwo ex but he hase a lot of bad matchups. After looking at some of mewtwo ex match ups i found its most viable to play mewtwo ex if you can use its second attack. So i would say its best to play him with gardiviore from nd. Here are the match ups i found to be bad aginst him.
Coballion from nv. Coballion hase resistince to psychich and you can attach a evolite to him and a special steel energy on to him to reduce more damage. You can run ruins of alph to help aginst coballion thoue
Reshiram from bw. Reshirams second attack discards two fire energys attached to him so this will make mewtwo ex x ball do less damage. And you can have a evolite attached to reshiram.
Chandelure from Nv. Chandelure first attach can really criple mewtwo ex and he hase his ability to put other damage counters on mewtwo. But mewtwo ex may be able to out speed this deck.
Zoroak from Bw. Zoroak hase resistnce to psychich pokemon and Zoroak can copy one of mewtwo ex attacks.
I know of more counters to mewtwo ex but there not played very offtenly