I don't see any real reason other than tradition that an adventure game has to make you play the same main character from beginning to end.

Why not make an MK3 adaptation with the Shaolin Monks engine, but split the story up and let you play each character's individual part in it as missions?

I.E.

In one level, you're Sub-Zero and Smoke, trying to escape the clan. The level ends with a cutscene of Smoke doing something heroic like "You go on ahead, I'll hold them off!" and getting captured and automated.

In another, you're Raiden and Stryker, and the thunder god is escorting the confused cop to Nightwolf's reservation to meet up with the rest of the heroes, while they run from and fight off extermination squads trying to catch them.

In another, you're Kitana and Jade, trying to free Sindel.

In another, you're...say, Kabal and Stryker, trying to destroy the Soul Chamber and set Earth's souls free again while the more powerful heroes go to challenge Kahn.

In the last level, you're Liu Kang and Kung Lao for the final battle against Shao Kahn.

You could probably map the entire game into missions like that, though it could get a little tricky sticking to a two player co-op format if, for instance, you had a mission where you're Reptile and Jade, hunting Kitana, then at the end of the mission, Jade turns on Reptile so Player 2 has to switch to and get used to playing as Kitana pretty quick.

And then there's the characters who're largely a loner like Scorpion and Kabal, their backstory could mostly only be told in one player missions or maybe even just cutscenes interspersed in between other characters' levels.

Like the game keeps showing you what Scorpion is up to and you're like "Dammit, when am I gonna get to play as him?" Then finally near the end he learns Subbie is one of the good guys, remembers his vow, abandons Kahn's side, and you finally get an awesome level of like Scorpion and Sub-Zero taking down the Cyberninjas. (Although it would be funny to have a Scorpion-and-Noob level before that, like Kahn or Quan Chi gives them a mission and Scorpion doesn't realize his partner is the dead version of his ex-worst enemy while Noob at this point has no memory of his old life so he doesn't remember Scorp is the one who killed him, but we the fans know so it's ironic for us.)

i had the same idea as well with the issue of spin off games , i never really wanted them to make a adventure game were they focused on 10r 2 main characters instead do like you said and split it into many characters, cause the MK universe has over 60 characters so making a game for each character would be forever to get the gist of everyones storyline lets look at all the good characters who had allys that worked as partners

lui kang and kung loa
sub-zero and frost (remember during MKDA they boths traveled together)
sub-zero and kenshi (MKD they had a mission together)
reptile and nitara
cyrax and nitara
kenshi and ermac
kitana jade and mileena (im sure they all worked together or in pairs at one point in their lives)
raiden and whoever he bring to help during these tragedies
kabal and whatever members of his clan kira kobra etc.
sub-zero and smoke
sub-zero and older sub-zero (im sure they had missions together )

i mean there is so many characters good and evil who had allys there is tons of story for a single game that can play in the MKSM style since when you unlocked the characters in the game sure they had different moves but they were still programmed like all the others they had the square basic attacks triangle popup attacks circle for the strong attacks then the special moves are the only real differences, so switching between different characters through out the game wouldn't be that big a deal or that hard to get used to playing those characters MKSM had a simple game mechanic but a very good one, especially the concept of leveling up your moves and combos. so much story can be told if done this way and with the WB giving them plenty of time and finances to develop this idea would defenetly work if done right.
being a person who studys game design i know this could work maybe not fit all 60 or more characters in one game but it could be done with maybe 2 games hell final fantasy gets to have over 4 discs just to tell their story why not MK have that same ability to have multiple discs though i think with today's tech that wouldn't be a big issue. plus since almost all these characters story tie them together most of the story can be told in short missions for these character pairings.

if this idea was fleshed out givin some real thought and time it would definitely be able to tell every characters storys in depth and be really fun game.

I totally agree with you man, That sounds like an awesome spinoff. I would love to see the centaurss invade the city first hand and kill Johnny Cage. That could have alot of potential.