Dang, I missed a lot.
Okay, let's begin with the New Mewtwo. What's the big deal? Sure, it would've quite nostalgic to see our beloved Mewtwo, but I think we're getting too upset over this. At least, that's what I'm seeing.
In my opinion, I don't mind. Besides, this new forme of Mewtwo's is part of the 6th Generation, so it will be incorporated into the XY games, somehow. So, Kalos is where you can see this form. Therefore, this Mewtwo may have existed outside of Kanto, created from Mew's DNA, and given the power to change forms with the help of the 6th Gen's Evil Organization. Again, this may be incorrect, but is a solid theory on why this new Mewtwo exists.