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How could this happen? Warning: content may cause blood pressure to rise
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This is true, as Mewtwo mostly serves to patch up holes in specialist teams, and would only be super-optimal during weather events or against pokemon with weak counters like ground and water - no longer an issue with Groudon and Kyogre.
However, don't forget that Mewtwo also makes a Psychic/Ghost specialist.
Seems like you should need to be at least level 20, if not level 30, to receive an EX pass. More than that though, one of the criteria should be that you have at least 8 gold gym badges. In Pokemon Red/Blue, you can't get Mewtwo until after you have collected all 8 gym badges and beaten the Pokemon League.