A Wario situation would be much appreciated.
But completely impossible to expect because the forms have the "tail" (in quotes because his forme's "tail" is on its head) in different places. In order to have everything the same (hurtboxes, animations, hitboxes, etc) the bones would have to be the same for both skins, meaning the tails would have to be in the same spot. As a result, if Mewtwo still used tail attacks in any capacity (which I imagine he still would) it would be impossible to work it out to have one or the other as a skin ala Wario.
And trying to apply the tail bone to where Mewtwo's forme's tail head thing would just cause janky animations and everything else. Not to mention the physics would turn out janky too. :x
Wario's alt works because none of his animations need to be altered to take into account his new alt. No bones change and no hurtboxes change either. It's literally just a new model that can be easily rigged to Wario's boneset. Mewtwo's forme (or the other way around) would not have that luxury.
The only way to have Wario-like alts is if they are like a situation with Mario and Dr. Mario: it's just a new model that has nothing new added onto it that would affect hurtboxes, hitboxes, or animations.