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Okay, one thing that is grinding my gears and destroying me from the inside, is the fact that Mewtwo is... not even Mewtwo. Everyone in my age, older and younger by some odd years HAS KNOWN WHO MEWTWO IS!!! A savage, clone of Mew, powerful, MANLY Pokemon. His voice gave us chills. He is the creator of cloned Pokemon (Mewtwo Strikes Back) and Ashes friend since Gen1.

But, yet, in this Genesect movie, Ash doesn't even know who Mewtwo is. As a matter of fact, I DON'T EVEN KNOW WHO MEWTWO IS. Who thought it was a great idea to show Mewtwo's protective, feminine side? They are basing these movies and new shows off of the games. The new generation wants to know why Ash and Pikachu are friends. How Ash is where he's at. By saying Ash and Mewtwo never met, is pretty much saying Ash just appeared in some random city with battling skills already.

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enter image description hereThere is speculation on weather the Mewtwo in the first movie is the same as the one in the Genesect movie.

  • Some people say that it is the same one, but as it speaks though telepathy so it can make it's voice sound how it want's to in people's/pokemon's minds.
  • The other opinion is that it is a different Mewtwo altogether, created in Kalos or an unknown region the same way the original was, and that there are multiple Mewtwo's around the Pokeworld. The multiverse theory also comes into this.
  • There is also the strong theory that the anime and all the movies are not connected in any way with Ash and Co, and whatever happens in the movies doesn't affect the anime or other movies, and vice versa. This resulting to making Mewtwo be whoever it wants.
  • There is also things to do with the production company and voice actors, of which I've not looked into too deeply.
  • Oh, and the reason Ash does not remember Mewtwo is because Mewtwo wiped all of the events that happened to Ash and Company at the end of the first movie, resulting in no one knowing who Mewtwo is.

In my opinion, I think Mewtwo had a female voice because Mega Mewtwo Y has a more feminine look to it, so the producers decided to make it that way. As for the multiple Mewtwo's, I personally think that there is only one. Although most people seem to go with the fact that there are 2, or more.
mewtwo y

This is quite a long answer but I hope this helped :)

Sources: Two Mewtwo's exist/ Details of multiple Mewtwo, and mutiverse theory/ Discussion on the subject/ More discussion/ A search on google and many things come up about this.

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This is to show off the new Mega Evolution, obviously. Mainly sort an advertisement of the changes introduced.

Also, it can be assumed that this takes place in an alternate universe on the whole. Funny, I know, but it explains how his age never changes.

Also, this has happened before, where Ash meets a Legendary once, but it is kind of forgotten, in a way. I guess that is to help with the story line. So as to the exact reason, should be better answered by the Pokemon Company, but this is what I feel.

All the originality is not lost though, as

>In the credits, a reference to the original Mewtwo is made when the Mewtwo in this film is shown standing on top of a building overlooking a large city at night. This is the same scene that the original Mewtwo last appeared in at the end of Mewtwo Returns.

from Bulbapedia

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The reason why Ash doesn't remember Mewtwo is because at the end of the first movie Mewtwo erases the events of everything that happened to Ash and Co, making him forget Mewtwo.
This is beautiful. I think you should answer this on your own, you may get the BA.
I've answered, hopefully people will find it useful :)