Shang typically eats the ninjas for breakfast, although Scorpion stands the best chance at escaping the meal...
Obviously, skull spamming doesn't work against Scorpion who can easily telepunch out of it. This doesn't mean that skulls are worthless; just use them in moderation to disrupt his style of play. Scorpion will be in the air a lot looking for throw attempts and teleports, so by all means throw a couple to keep him honest. Punish blocked teleports with 3x skulls. In close quarters, however, is where Shang excels. Once inside, Shang can kara-jab Scorpion to death; ESPECIALLY in the corner where teleporting is impossible. If all else fails, morph into Kang and low toe FTW.
Scorpion can counteract the skulls with a telepunch, but other than that he needs to be wary of Shang's deadly CQC game. When in close, look for crossover attempts that can result in either an air throw or a deep JK then spear. If mid-screen, follow the JK with a telepunch, spear, uppercut. Simply jumping in against Shang from mid screen is going to result in an aaHK. Look for counter opportunities when possible and pray Shang doesn't morph into Kang or Jax.
Shang would win this match by himself anyway, but throw in the morphing and he has a dominant edge. 7-3 Shang.