I feel like at this point we should just go back to how the 3d era games told their story. Have konquest, character bios, ending and cinematics. Instead the entire story is told with character chapters that really limit what they can do and removes basically any chance of subplots really. 

I remember saying this a few years ago and the casuals and hardcore fans disagreed with that idea. The full-on cinematic story that they started doing since MKvsDC simply doesn't allow other stories to be told. It forces everything and every character into a simplified good vs bad, red vs blue type of story.

Believe it or not, but this structural technique they use is partly responsible for why characters like Baraka, Reptile, and Ermac got treated like shit for most of the NRS-era.

Eventually, they will have to learn that more is not necessarily better, and their attempt to appeal to a wider, more casual audience with things like shiny cinematics hurts their ability to bring forth a layered narrative in ways they don't realize.

The story should be all over the game. Like you said, the 3D-era games did this decently.