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Apologies if this is a broken record, was talking about it in another thread before it was archived.
I am also one subscribed to the thought of there only being ONE Mewtwo, whether it's game's plot line with Red that then potentially lead to his "appearances" throughout the other Gens or the anime's "First Movie" and the direct-to-video sequel with Giovanni.
(The Genesect movie made no sense, more so to how it was first advertised as if Ash knew who Mewtwo was, but it was also during the shows shitty variation of the Black and White gen which is probably the reason why)
Interestingly enough however with Detective Pikachu, during the credits, Mewtwo's voice is listed as two actors, both male and female.
This was most likely to give more emphasis on it's telepathic voice effect but could have also been a choice to put emphasis on "legendary" pokemon being "gender less".
So despite what I said prior, and how Mewtwo with a guy's voice will most likely be always the more remembered variation, it is a pretty neat idea.
Definitely not something I was expecting to come from Detective Pikachu of all things Pokemon related. So kudos to them I guess.