Johnny Cage was really entertaining in the story. I liked him a lot; glad he didn't die like in the last timeline. Nightwolf was surprisingly badass, and I like the how Lin Kuei played a much bigger role than they did in the past.
Sub-Zero and Scorpion both displayed the most humanity out of almost all of the characters. To the person who said Scorpion was too easily manipulated, do people forget that Scorpion is not only immortal, but a tormented spectre? He has all the time in the world to pursue his targets, and the weight of having to bear the loss of his kin of his conscience is similar to Reptile's absolute desire to revive his extinct race at any cost. If you had to bear that kind of stuff on your conscience, wouldn't you do anything to put your soul and mind to rest?
Also, Mileena will play a much bigger role in MK10, due to her being the heir to the throne, both Shao Kahn and Shang Tsung dead, and Shinnok and his armies trying to take Outworld.
Also, even though I'm a Sektor fanboy, I gotta give it up to the story writers for increasing Cyrax's character development, although I wish they would give Cyrax and Sektor real names like they did with Tomas Vrbada, Kuai Liang, Bi-Han, and Hanzo Hasashi.
I love both Jade and Smoke, but their character development needs to go beyond "Kitana's friend" and "Smoke's friend". Kano was probably the most entertaining villain story-wise, even if IMO his voice sounded kinda forced at times.