I overall really liked the story; played through it in two sittings. Reading the Mortal Kombat X comics, and knowing a lot of the previous timeline's story helps as well.
After the first story trailer, there was no question that Story Mode was mainly meant to set up the new generation of characters, specifically the "kids," so in that sense I got what I expected. The narrative for Mortal Kombat (2011) was more well put together, but Mortal Kombat X's has better production values.
I was completely unsurprised that Shinnok was the main villain as that was set up at the end of the last game. Kotal Khan was never meant to be a power like Shao Khan, and the current "administration" of Outworld is not blood thirsty conquering warlords like under Shao. Kotal is not as strong as Shao, but is a better "leader" that actually cares about his Realm. I thought his character was done well, and NetherRealm said several months back he is not meant to be an antagonist like Shao was.
I did find the Outworld Civil War plot to be the most interesting, and thought Mileena was exceptional in the game. I'm not surprised Goro is absent from the story, as Kotal tore off all his arms in the comics. I don't see Goro getting Robo arms like Jax.
I did not see D'Vorah's twist coming, so that was awesome. I also expected Liu, Kitana, and Kung to be "saved" since they have different skins in the roster, so that was a surprise and an interesting twist to their characters. Dark Raiden was also a great surprise.
Overall, I really enjoyed the story, and hope we're able to learn more and not have to wait until the next game, as there's lots more I want to know.