Going out on a limb now. Ok so Canonly Mewtwo destroyed the place he was created, both in the games and in the anime, so majority of the data has been erased.
What is Newtwo (saw someone call the new Mewtwo thing this), is another Clone of Mew and not Mewtwo?
What ever evil team tried to reinvent the data used to create Mewtwo, but because most of it was destroyed they had to constantly test and tweak the clones. All of them until recently failed.
Now, the Newtwo was created, but since the original data was destroyed he came out different than Mewtwo. Hence why they share the same color scheme, but have different body types. Who ever was incharge attempted to create another ultimate life form.
I can honestly see this Newtwo having stats between Mew and Mewtwo (between 600 and 680). If not a carbon copy of either Mew or Mewtwo. If Mew copy, then it would either have a seperate stat distribution instead of straight 100's. If Mewtwo then it could be higher in defense and lower in attacks. It looks more sleek and speedy too.
Same experiments don't always yield the same exact results. I'm thinking this is a new Mew Clone in an attempt to correct the mistake made with Mewtwo.