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