Mewtwo in the new movie is not the same as the old movies. It was created by different people, likely team Plasma, but we are unsure. The new mewtwo, who I will refer to as newtwo is presumed female, and mewtwo as a male.
A couple things to note, they use telepathy to talk so their voice may not mach their gender but it is likely that they use a feminine or masculine voice to avoid confusion. A common misconception is that mewtwo is genderless and there can only be one. Mewtwo was cloned, and therefore can be cloned again. Even if the original lab blew up, there still exists the technology to do it again. Also, mewtwo is in the undiscovered egg group. This does not mean they are genderless, but rather the Pokemon scientists are unsure as to how they breed. This is shown in the games where we see Solgaleo and Lunala create another cosmog, as seen here. https://youtu.be/6x4wJNI51FU?t=140 And in the anime a baby lugia is seen as well.
So, to answer the question, it is a different mewtwo, and newtwo is most likely female, or the female kind of however it is they reproduce.