I liked it. Sure, it had it's faults, but on the whole, I think they told a pretty solid story.
The Good:
Cassie Cage: I loved her even before going into the game and my affection for her only grew after playing the story. Not only is she funny and bad-ass, but she had more depth to her than I expected. In fact all the characters who got a chapter did.
The Cage/Blade Family - When I first heard that Johnny and Sonya was divorced in the current time of the story, I was a little disappointed. But after seeing how they played it out, I thought it was really touching. Sonya was the one to mess up in the relationship, which was something I wasn't expecting. In an unexpected twist, Johnny was the loving husband and father and Sonya was the one who let her career get in the way. And, as the story progressed, we saw her make steps at repairing the damage until the end where we saw them reconciled and a family reunited.
Jacqeda - Romance has been a part of MK for quite some time and it's nice to see it again in MKX. And what makes it even better, IMHO, is that they avoided the predictable. Instead of pairing Cassie with Takeda, which most had expected as they were both someway related to characters considered to be the Faces of MK, NRS chose to put Takeda and Jacqui as the Johnny and Sonya of MKX.
Scorpion No More - It was real great to see Scorpion progressed beyond just being a vengeful wraith. Hanzo Hasashi has always been a very interesting aspect of the Character and I loved getting to see that explored.
A World of Greys - Instead of having a straightforward Good vs Evil story, there was a lot more grey to this. The welfare of Outworld was what put Kotal Kahn and his group at odds with the Earthrealm heroes, not a desire to conquer or just because he was evil. Tanya was motivated by seeing a Free Edenia restored. Mileena wished to regain her throne out of a desire to bring honor to her late father.
A New Power in Netherrealm - With the death of Quan-Chi and the gruesome fate of Shinnok, Liu Kang and Kitana have assumed control of the Netherrealm. This entrigues me greatly. For the first time in a long time, both characters are being brought in very interesting directions.I can't wait to see where it takes the story.
The Bad:
Kotal's Krew - With the exception of D'Vorah and maybe Erron Black, Kotal's underlings weren't given much of a story or even a personality. They were just there to get their butts handed to them in a fight, which is a real shame. I would have liked to have seen all of them explored at least a little, or at least given some importance to the story. I mean Ferra/Torr only appeared in two scenes and that was it. They wasted an awesome concept by reducing them to simple lackeys.
Kung Jin - This one is a very subjective problem and I admit it wholeheartedly. Kung Jin is annoying AF. Sure, they give him some redeeming qualities and he comes off as likable in the end of the story, but the majority of it, he's just acting like a jerk, and not even a likable jerk like Johnny from MK9. He gets his team into trouble multiple times and is completely unapologetic about. I found myself wanting to slap upside the back of the head.