Shao Kahn is the Emperor of Outworld known for his godlike strength, extreme brutality and knowledge of black magic Like his subordinate Shang Tsung, he has the power to consume others' souls. Later in the series, his abilities are toned down to make other bosses appear superior.
Unlike Shao Kahn, Shinnok relies less on brute strength and fear-mongering, but more on magical powers and ancient artifacts. He is the ruler of the Netherrealm, possessing millions of years' worth of knowledge and power, including the ability to perfectly impersonate any other beings of his choosing, as well as to transform into an immense demon. He also possesses extreme cunning, as well as the ability to manipulate events through others.