It'll be the same way it has been in the first 3 games.

Because I don't have work today...

MORTAL KOMBAT

Good Guys MK1
Raiden
Liu Kang
Johnny Cage
Sonya

Neutral Guys MK1
Sub-Zero
Scorpion
Ermac (If you consider the Error Macro in MK1 to be cannon)

Bad Guys MK1
Shang Tsung
Goro
Kano
Reptile

MORTAL KOMBAT 2

Good Guys MK2
Raiden
Liu Kang
Johnny Cage
Kung Lao
Jax
Sub-Zero
Sonya (Chained to a pedestal...but hey she was still there)

Neutral Guys MK2
Smoke
Noob Saibot
Scorpion

Bad Guys MK2
Shao Kahn (Uhh,,,,duhhh)
Kintaro
Shang Tsung
Reptile
Baraka
Mileena
Kitana (Starts off bad but turns good at some point in MK2)
Jade

MORTAL KOMBAT 3
Gonna list the Ultimate version because uhhh it was ULTIMATE

Good guys UMK3
Liu Kang
Kung Lao
Sonya
Jax
Sub-Zero
Nightwolf
Stryker
Kabal
Kitana

Neutral Guys UMK3
Noob Saibot
Robot Smoke

Bad Guys UMK3
Shao Kahn
Motaro
Shang Tsung
Sindel (Turns good after UMK3 when Shao Kahn's beaten)
Mileena
Jade (Starts off Bad but then turns good)
Scorpion (Works for Kahn but when he sees Sub-Zero he turns on Kahn and goes back to being neutral)
Ermac
Reptile
Rain
Sheeva
Cyrax (Starts off bad but Sub-Zero turns him into a neutral character)
Sektor

And that's all she wrote