They are fictional characters. They haven't "earned" anything. They don't "deserve" anything. They only do what the devs make them do. Scorpion and Sub-Zero's popularity is not something the two of them have earned. They were designed by real people, they are the ones who take the credit, they are the ones who deserve it.
If Scorpion and Subbie get to be main characters in a game, it's not because they deserve it. It's because the developers chose to make them so, because they want a story to be told with them in the lead.
I would just prefer it happened in a non-canon spin-off, because they have never had such importance in the main games. As I mentioned earlier, their stories were personal side-stories that had nothing to do with the main plot. They are shove-ins into the story, always have been, because the MK team needed some excuse to make the two most popular characters relevant enough to be put in the game, even if that relevance is minimal.
Scorpion is no hero. He has only ever been concerned with himself. If he ever killed a bad guy, it's only because they got in his way. He didn't kill Quan Chi because of some heroic act. On the contrary, he killed him off for selfish reasons, and didn't care about anyone else. Raiden and the others needed Quan Chi so they could free the other Revenants from his magic, but Scorpion didn't care about that one bit. Because he is a selfish moron who only cared about "REVENGE!!!" And now that Quan Chi is dead, so has Scorpion's relevance to the main story died.
Sub-Zero, however, have shown some redeeming qualities, but has been all too wrapped up with the Lin Kuei. But now that he is the Grandmaster, he has offered aid to the main heroes, but for some reason won't get directly involved... until he does. That last scene where he takes the Lin Kuei and attacks Kotal Kahn and the other Outworlders to save Cassie and the team was him taking a step into being directly involved with all the otherworldly affairs. Whether or not NRS wants him to be more involved is something we just have to wait and see if happens.
Sure, NRS could write a story where the two of them team up against some bad guy. I just don't see any reason why other than pandering to slobbering fanboys who are ready to suck their d!cks. It would be a money-grab, nothing more.
Oh, and before anyone says anything... I have never denied their popularity. They are just incredibly overrated.