Nether Realm Studios needs to fire whoever came up with boss immunity. He or she is not a human being.
The tip to beating Shao Kunt is this: Play Dirty.
My tips for the boss character fights:
Liu Kang vs Goro: I wanna ride mah bicycle I wanna ride mah bike all day long.
Liu Kang vs Samsung: see above.
Kung Lao vs Kintaro: Spam Square, seems to be something he has a hard time blocking.
Liu Kang vs Shao Kunt: Jump away from him, spam low fireball, if he gets close, jump away rinse & repeat.
Stryker vs Kintaro: Combo the shit outta him.
*special* Sub Zero vs Goro&Kintaro: Square Triangle Square, combo spam that and they'll go down.
Raiden vs Shao Kunt: Jump away, wait for Taunt/Spear throw, teleport, uppercut rinse & repeat.