I suggested NPC fights during story mode back when Tanya was pretty much deconfirmed as DLC for MK9. This was mainly because I wanted the Dead Characters to stay dead and unplayable, but at the same time I knew they needed to be in the story. Plus, I really hate it when characters who are crucial to the story of a game are literally absent in the game. This was one of the big problems with the 3D Era games (specifically MKDA-MKA). Tanya was important to the story of Deadly Alliance as per her Deception Bio, yet she wasn't in Deception. Fujin became the protector of Earthrealm in MK4, but he's literally nowhere to be seen until Armageddon.
Yes, MKX still had this problem (specifically with Fujin and Jade, slightly with Knightwolf), but they did atleast address the fact that the other characters still exist and are active in the story, and hopefully they'll have enough of a budget to perfect that formula for MK11.