To see Jade as a Revenant, and to fight her, Stryker, Kabal, Nightwolf, Smoke and Shinnok's demons.

Made the QTEs much harder. The creatures encountered in the krypt were a lot faster.

Kept Jax as a Revenant longer, or for the whole story. That design was just awesome.

Remove Sub-Zero's chapter, and make the fourth one about somebody else, like Reptile, Erron Black, Ferra/Torr, Kano, Ermac or Mileena. Sub-Zero's already playable anyway, and his chapter was only about testing the newbies.

All three Shokan should have been encountered and fought, as well as Frost in Scorpion's chapter, and Skarlet.

Explore Sonya's relationship with Cassie more. Explore Sonya's relationship with Jax more. Her chapter was fantastic but it did feel very contained considering the many facets that could've been explored and probably should have been explored through her rise from lieutenant to general.

Mileena got shafted. I would've liked to have seen more of her as Empress in order to justify her grizzly execution.

I also would have liked a little more closure with Sindel. Her slaughter of the heroes in MK9 was a big deal with a huge effect on MKX and the most it really got was a short warning for Cassie before their fight.

I think MKX had a great story though. There was just far more stuff to be addressed for one game.

I would have Smoke be cleansed after Sonya kicked Quan Chi's testicles off of their tubes that connect to the body.

I want Smoke back :(

Flesh out the Outworld subplot a LOT more, give Ermac and/or Erron Black their own chapters.
Definitely not make the Kombat Brats the front and center of the whole damn story.
Also ditch some of the non-playable cameos that were put in as nothing more than fan service.