Because Reptile had nothing to do with Mythologies plot.

the game mk:m sub-zero is about him before the mortal kombat tournaments. Its a history about how he came to the tournament before scorpion killed him.

Reptile was mostly associated with shao kahn and shang tsung. The only character not from earth realm or had evil intensions that was dealing with sub-zero directly was quan chi, who wasn't working with reptile till mk4.