I wouldn't be so sure about Sub. I want him to be good, but I know this game is full of twists and betrayle. But I hope he stays good. Anyway, this is my reasoning:

Nightwolf = good(given)
Kenshi = good(given)
Bo Rai Cho = good(given)
Ashrah = good(given)
Jax = good(given)
Sektor = evil(given)
Mileena = evil(given)
Baraka = evil(given)
Skab = evil
Kira = evil(most likely)
Noob Saibot = evil(given)
Li Mei = good(Although she's probably under control of the dragon king, fighting her allies against her will)
Ermac = good(most likely formed an alliance with Kenshi, and he's displayed noble behavior in the past)
Sindel = good(She's no longer under Kahn's control, and her MK3 ending hinted at her previous just nature)
Smoke = good(Since he's most likely joined with Subzero's new, positive Lin Kuei, he's probably good)
Subzero = good(is the story stays consistent, he'll remain with his current alignment)
Scorpion = good(My theory is that he was purified in the heavens)

If my theories are correct, we won't have many villains this time around.

my ideas:

Liu Kang: bad(a loss soul under the DK control: theroy sub boss)

I think Sub-zero is bad. He may have somehow become part of the "Deception".
Any red dragon charcter like Kano or this new red dragon memeber Kira are bad.
Not sure about the rest of the cast.

i hope ashrah and li mei are evil.

My Thoughts-

Nightwolf = good
Mileena = evil
Baraka = evil
Subzero = evil (under control of DK)
Kenshi = good
Bo Rai Cho = good
Ashrah = neutral
Jax = good
Sektor = evil (see MK:Te)
Skab = evil
Kira = evil (the black dragon are bad)
Noob Saibot = evil (he killed Goro)
Li Mei = evil (under control of DK)
Ermac = evil (betrays kenshi)
Sindel = good
Hotaru = neutral
Smoke = good
Scorpion = good

Sub-Zero - Good (He is a protector of Earth Realm, he returns to Outworld to battle against the Red Dragon and the Dragon King's army, he also battles against the unknown Tekunin led by Sektor.)

Liu Kang - Evil (Liu Kang was brought back from the dead to serve the Dragon King.)

Scorpion - Neutral (Scorpion does not care about the struggle between Earth Realm and Outworld, he wants his revenge.)

Kenshi - Good (Kenshi returns to Outworld with the aid of Ermac to bring down the Red Dragon and take the Dragon King away from his throne.)

Baraka - Evil (Baraka joins forces with the Dragon King with Mileena, Baraka betrays her in exchange for raw power at the hands of the Dragon King.)

Bo Rai Cho - Good (Bo Rai Cho returns to aid the Earth Realm warriors in his native land of Outworld, Bo Rai Cho is a guide to all of the warriors and will help bring the destruction to the Dragon King.)

Mileena - Neutral (Mileena first joined forces wit h the Dragon King untill she was betrayed by Baraka, Mileena joins forces with Sindel to rescue Kitana and kill Baraka.)

Sindel - Good (Sindel travels to Outworld after her daughter Kitana was captured by Liu Kang. Sindel was ambushed in the Outworld by the Dragon King's army and her soldiers that went with her were all killed, Sindel is alone and must use her fighting skills to save her daughter and return to Edenia.)

Ermac - Good (Swearing an oath to protect Kenshi, Ermac returns to aid Kenshi in combat.)

in the concept drawing she doesnt seem evil

GOOD GUYS:

Nightwolf
Kenshi
Bo Rai CHo
Jax
Sindel

NEUTRAL:

Hotaru
Ermac
Scorpion

BAD GUYS:

Sektor
Liu Kang
Mileena
Li Mei
Noob Saibot
Baraka
Sub-Zero (under control I hope!)
Ashrah
Kira
Scab

lui Kang:bad a$$(brought back to "Decieve" earth realm
Kenshi:Good
liemei:bad a$$
baraka:Neutral(taking his revenge on Quanchi)
Kira:bad ass
meleena:bad ass
noob saibot:good(killed goro on purpose to help earth realm)



these are my thoughts!!!