The UST between Johnny Cage and Sonya. At first, Sonya is dead set against responding to any of Cage's advances, and even slaps away his hand when he offers to help her up after their spat. When he saves her from Kano, though, he offers his hand again, but pulls it back a bit after remembering what happened the first time. Sonya then smiles and willingly offers her hand, and becomes more open to him after that.
And if that wasn't enough, Mortal Kombat X reveals that, after all is said and done, they have a daughter, Cassie, implyimg that they got together, if not married, after the reconstruction of Earthrealm.
Cage also showcases his Jerk with a Heart of Gold tendencies in his chapter by averting the gruesome tendencies that the game is known for. When told to "finish" his opponent as is custom, Johnny's reaction is to first laugh it off as a joke, then express horror at the suggestion, affirming that he will not kill someone else.
Also, Liu Kang after fighting Kitana. He acts like a perfect gentleman after the match even though she tried to kill him, and even does her the favor of acting like the fight never happened so she wouldn't get in trouble.
When Cyber Sub Zero saves the soldiers. Not only does it double as a moment of awesome for him, since he took out Goro and Kintaro in a tag match, and devastated Ermac immediately after that. In the cutscene that follows, the soldiers surround him and shower him in praise, thanks, and admiration. It's doubly effective since Subby just admitted to feeling rather guilty at all the horrible deeds he did while Brainwashed and Crazy, so it's nice to see his good nature shine through and rewarded in such an effective way.
Speaking of which, in the intro for his chapter, what is the first thing he sees upon having his free will restored? His friend, Smoke.
Kratos' Arcade Ladder Ending, probably the first time a God has showed him any form of respect or did not backstab him in the end. The narration stresses how surprised and unused to this the Spartan is.
Kitana's Arcade ending qualifies too. She takes pity on Mileena, since they're technically sisters, and the two of them, along with Jade, team up to protect all the realms from future threats. Doubles for Mileena, because she actually follows through with it.
Chapter 10 in the Story Mode is Jade. Just before it starts, she decrees she will help Kitana, breaks into the Tower to rescue her, and states when confronting Mileena that "she is more a sister to Kitana" than her.
Stryker and Kabal get a co-worker and bromantic relationship, and it's clear they care for each other immensely.
During the Earth invasion we see Johnny Cage under stack by Motaro. Those familiar with the original timeline know that this is where Johnny dies. However when Raiden spots them he immediately flies over, electrocutes Mortaro and then slams him through the bridge! This is perhaps the biggest change Raidan makes to the timeline and it shows how deeply he cares about his warriors, how many can claim they were saved by direct divine intervention?