Allow me to put on my tinfoil hat for a second:
In MK9, in the scene where Kitana meets Mileena for the very first time, you can see what appears to be two fully-functioning Tarkatan-Edenian hybrids, the one on the table that we've come to know and hate love, and another that's still in her test tube. Now, i don't know how far ahead Neatherream's writers have planned things out, but what if the Mileena in that test tube is the one that can return in MK11?
Now, it's a hell of a stretch, and one that could be written off for a variety of reasons ('test tube Mileena expired over the 25 year time-span.' 'She wasn't actually a fully-functioning clone'. etc, etc), but looking at it from a visual story-telling standpoint, why show two? Why not have all the test tubes be filled with obviously failed experiments so that we as the viewer can clearly tell, 'Alright, this one Mileena is clearly the only successful experiment in here.'
It could be a red herring, it could just be an oversight, but I have a gut feeling that NRS was counting on most of us completely forgetting about that Mileena in the test tube so that they can surprise us with her appearance in the next game.