In the Japanese version of the first movie, Mewtwo's voice is explicitly masculine. Also, if you remember correctly, in the end of the movie Ash and friends completely have their memories erased of the events that happened. So why in the trailer, does Ash say "Mewtwo" ?
I'm thinking the form change and feminine voice are indicating that this Mewtwo is a different Mewtwo. Perhaps someone made another one, and this one is more female-oriented? The new form in itself also does look more feminine to me. Plus the fact that the games are X/Y, which are the gender chromosomes.
Really, don't get all upset, we really don't know hardly anything! They're teasing us good enough to keep things veiled. :0
I don't get how this should change your opinion a genderless pokemon that is a scientific experiment created by team rocket. Let's keep in mind you are hearing the JAPANESE version, where most of the voice actors for male characters ARE GIRLS. Knowing America, they will most likely change Mewtwo's voice to more masculine. Plus, this Mewtwo could also be not the same Mewtwo from the First movie and Mewtwo Returns. They could easily try to recreate the failed experiment. I believe a lot of people thought Zoroark was going to be masculine in that movie, but it's a girl as proven in the games when using the shiny legendary beasts.