Quoted By:
I like both of them for different reasons.
Y is essentially Mewtwo tapping into his own genetic "Parent", further diminishing physically as its psychic power grows to the point where mundane strength and stature is no longer necessary. In order to better contain its vast intellect the mass from its tail is redistributed to its skull, allowing its brain room to expand. It no longer needs a tail for balance because it now simply moves everywhere through levitation.
X instead builds upon its own inherent physical advantage over Mew, further distancing itself from her in an attempt to become its own unique being instead of merely a clone of the original. The mass from its tail is redistributed more evenly around its body in the form of thick skin and protruding bone armor, and its musculature becomes more pronounced. In order to compensate for diminishing the structure of its feet is altered so as to better maintain balance without having to rely on psychic power.
I'm getting X for the other exclusives, but I can definitely see the appeal in both.