This has been explained before. He never once stated this Mewtwo was the same as before, his statements were just worded in a way that made it a bit unclear whether he meant this was a different Mewtwo, or the same Mewtwo who had been changed by its more recent experiences.
I'm not sure where the translation Crimson Blazer quotes comes from, but it's not a correct one. It was explained back in February what he had actually said.
Also, him stating he "felt it would be better if this was a different Mewtwo" is him talking as a director. It fit the story better for the Mewtwo to be a different Mewtwo. It really isn't something to get so hung up about.