Most of my issues with the story are very minuscule, as it's just things that were kinda overlooked:
-Kotal Kahn's takeover happened in the span of just minutes. It wasn't even entirely planned, Mileena just heard them talking smack then Kotal and friends beat them up and Kotal was made ruler. I think it would have been much better if Kotal was given a flashback chapter where you played as his early self, and you went through events that lead to him overruling Mileena.
-Sonya beating up Quan Chi was to keep Johnny from becoming a revenant, but after she steps on his gonads, Sub-Zero, Scorpion, and Jax are all freed from his control, yet when he is decapitated by Scorpion, the other revenants are not freed. You can argue that it was Quan Chi's will that was needed to free them, since (I forgot who) was telling Scorpion that, but Sonya beating the mess out of him seemed like they were freed by force. It's not like Quan Chi told her to stop, and then freed them by his own choice.
-When D'Vorah beats Rain and Tanya, she was going to kill them but Cassie steps in and stops her, yet when Mileena is being executed Cassie and others don't do a thing about it, and Cassie just simply makes a, "That's gross" comment.
-I feel there's a little inconsistency with the revenants. Liu Kang's revenant seemed completely self-aware along with Kitana's, but others sounded like they were fully being controlled, like the simplicity of Jax's wanting to kill Johnny and Sonya. But when Kitana's mentions that she can't be pushed around anymore, Jax's response makes it seem like it's Kitana's true words. Also since Jax was a revenant himself, it just seems more likely that they are, as Sonya stated, he knows a lot about Quan Chi due to being forced to serve him.
There's a few other things like this that I can nit and pick at, but besides the painfully predictable ending, there were no huge problems for me in the story. I do still like MK9's more though, but that's because I loved how it was a retelling of MK1-3.