Shoggoths, as I've said before, are the perfect soldiers: basically indestructable, massive, acidic to the touch, can force it's body into any shape it desires (or is ordered to), follows any order without question, and to top it off, it would easily strike fear into the hearts of my enemies. They're a bit slow, but meh, who cares?
Also, they're technically neither good nor evil: they simply act on instinct.
If I can't pick a Shoggoth, probably Scorpion or Reptile.
While I like all of the MK ninjas, Scorpion and Reptile have always been my favorites.