Why does Quan Chi do anything? Maybe he just likes Sub-Zero Classic and New Jax?
Because MK4 thru MK9 history has shown that Quan Chi tends to resurrect people as
"not-quite-themselves" and brainwashed to serve him, and MK9 has shown that those who he keeps dead stay in their original form.
Look at Sindel and Kitana in the MKX story trailer, where Cassie is fighting off Sindel.
They're still the same way that they were in MK9, and Quan Chi hasn't resurrected them at that point.
Kitana probably escaped somehow during the NetherRealm war, thus she wasn't resurrected into a new creation by Quan Chi, and was able to return as herself, with normal pupils in MKX.
The ONLY explanation I foresee for Kuai coming back human is that he somehow escaped along with Kitana and Kung Lao, and later got the MK GOLD Cyrax treatment.
Otherwise, it's more likely that 1 of 2 things happen: (1) he will stay in the same form in which he died (cyber) and under Quan Chi's control or (2) Quan Chi will give him a new body as a new resurrected NetherRealm creation with new powers, and he will later somehow get cleansed.
The easier explanation for me than scenario #2 is that Bi-Han survived the Soulnado, and his divided soul (Bi-Han and wraith) gets separated, cleansing him in the process and still leaving the possibility of a purely evil Saibot who ends up ruling the NetherRealm after Quan Chi and Shinnok are stopped.