I didn't care for too much of the Trilogy nostalgia factor, character-wise.
While the Pit was nice, I would have liked to have seen some more post-MK3 stages as DLC (MK4 Prison, House of Pekara, Slaughterhouse).
Speaking of post-MK3, I also would have liked to have seen either more new characters and / or post-MK3 characters.
I'm glad that Stage Fatalities were patched in for The Kove (favorite Stage Fatality) and Refugee Kamp, but I also wish that they would have done a Stage Fatality for The Outworld Marketplace, Kuatan Jungle and NetherRealm stage.
For me:
Gameplay-wise, it's MKX.
Story-wise, it's MK9.
The story felt like the team didn't know which way they wanted to go with it.
Kotal Kahn felt totally useless, as far as story goes.
He becomes the ruler of Outworld and invades EarthRealm which is already under attack by Shinnok, anyways.
It made it feel like Shinnok was the bigger fish to fry, with Kotal being an afterthought.