but... what if... we could use the cloning machine to gain pokemon with the clone texture?
put a member of the following evolutionary families in the cloner:
Bulbasaur, charmander, squirtle, or pikachu into the clone machine in place of mew.
you will get the base form (though pikachu will only produce pikachutwo) of whatever you put in, with clone defects!
the defects are simply a texture change, but it would help add some varity and roleplay elements in. though i will say: pikachutwo will have slurred speech. and to make up for the fact that it can't evolve, slightly higher stats than a normal pikachu.
while we're at it: mewtwos armor from the first movie could be given to mewtwo as a held item. the effects are: lower attack/special attack and speed while increasing the defense/special defense and giving mewtwo a new look with a more robotic voice in response to being in the armor.