Then probably clones are enough to fix, it makes it even easier and faster xD
With the hands, same thing. Smoothness is cut because between the 2 surfaces, there's not 1 line of vertices, but 2. I mean, each vertex in the joint isn't just 1, but 2 vertices in the same place. While chest wouldn't need to be together with the arms, the different parts in the hands or head would need to be fused. Same to the tail with the rest of the body.
The UV XForm modifier will help alot, you can double the size of a texture, add the new one to the side, and just modify the UVs by halving the size, and moving the offset accordingly.
About UVs, if you use that modifier and resize the U and V sizes to, for example, 0.998, and you apply an offset of 0.001, you will probably get rid of those separations between symmetric parts. Apply the same to each part with that problem, and see if it's fixed. If the number isn't okay, just try another, being the offset (1-number)/2.
Cheer up, Mewtwo's gonna be really cool
EDIT: Oh, another idea. If you flip the U coordinate with that modifier again for the cloned shoulder, you may get the inverted thing. I mean, you could be using the original unflipped texture again. And you could even fuse both shoulders into 1 again
Also, another recommendation. Change the names of the textures/materials/objects wisely so it's more easy to find what is what.