>>12994338He says おまえは…。, which is literally "You are..."
Just like in English, "You are?" would be a question asking for the other's identity, while "You are...!" would be a surprise exclamation at realizing who you're looking at.
There's no question mark, so the intention is most likely the second, meaning that he did recognize Mewtwo. And I wouldn't trust WPM's ability to recognize tonal differences in Japanese for the life of me.