Pokémon X and Pokémon Y

It's not illogical.

Mewtwo is a clone of Mew. It makes sense that as Mewtwo "awakens" and becomes more powerful, it becomes more like the original pokemon that created it. Mewtwo is transitioning from a man-made pokemon into it's own species, and therefore looks more like a pokemon and less like a human.

This makes me like the new mewtwo even more, especially if that's the reason why.