Mileena is too soon.
Shao Kahn only considers about making an evil version of Kitana, Milineas later when she starts to show indications that she can align with earth realm, the fact that she could speak freely, think freely and disagree with that he had planning on top of having a royalty status is what makes him order Mister Shang Tsung to bake up an evil clone in order to kill her and replace her, he got the clone part, he just never got to kill kitana.
I think Argus and Delia are a bit too far as they are elder gods, but Taven and his brother Darius could be good at this part of the plot, Gorbak over Goro would be good as well, if they are really going from the begnining.
The Great Kung Lao would definitely be the MC in the story.
You can Replace Scorpion with the Shirai Ryu founder, Mister Takeda Himself (Not Kenshi's Son)
And Sub-Zero can easily be, Bi-Han and Kuai Liang's Father, as he is also an outworlder would be cool to explore the Sub-Zero Archtype, since Frost is more of a Cyber now (meh)
I'd also say Bo' Rai Cho but a Yonger Version of Him.