1st: Sub-Zero (Kuai Liang).
He had the most character development and the best story out of any character leading to Armagedon. I hated when in the new timeline they turned him into a fridge just for shock value (it didn't have any effect in the story and was done just to change random stuff for the sake of it, it happened out of stupidity given how Raiden didn't have any problem helping Smoke, they probably planned to kill him from the beginning so they could easily revert that nonsense which shows that the writers knew it was a stupid decision made for shock value) but now he's back to his human form and got the scar again (plus taking a very similar path to the original timeline) so we can act like the fridge stuff never happened.
2nd: Sareena
Probably her relationship with Kuai Liang from MKDA (GBA version) to MKA (her bio covered a lot of stuff, given her a lot more background than many other characters in the cast) is what made me like her originally, but she's a very cool character on her own, the backstory of a netherealmer figuring out she can be a force of good despite her origins and fighting for it is one of the best out of the cast even if she didn't have too much spotlight. I was hoping to see her interact with Kuai Liang during MKX but I guess I'll have to wait. The next time she is playable (hoping for DLC but probably next game) I hope with the variations they can show her alternate form.
3rd:
This spot is hard to pick as there are many characters that I like a lot after my top 2 characters: Kenshi, Kung Lao, Johnny Cage, Noob, Quan Chi, Sindel, Reiko...