I really dont think Kotal Kahn and Shao Kahn are related. First of all, Ed told us about Cassie Cage being related to Johnny and Sonya in that she's their child. If he mentioned that, why wouldnt he also address Kotal Kahn in a similar fashion? Second, Kotal Kahn is a god (as seen by his variations of sun god, blood god, and war god.) If I remember correctly, Shao Kahn isnt exactly a god. I mean he IS the son of Shinnok and brother of Raiden, but Ive never heard of him referred to as a god, so I dont think Kotal is Shao's son.
My guess is that hes an elder god or a protector god of Outworld, but Im not sure. His attie and weaponry all look like theyre taken right from Earth's Aztecs and Mayans. Im sure he'll be an interesting character nevertheless.