Whilst I can see where people are coming from with these questions, and I have a few myself (many of which have already been asked here) Honestly, I think it just "is what it is"
They wrote a story, had a zillion characters, tried to squeeze it together based around 30 odd fights and only 12 locations, tie it in with a comic, then had an obligatory boss fight and a 2015-friendly post credits teaser. Power balances were all over the place, people came and went, and some entirely no-showed. They had to make all this alongside everything else involved with the game and with Warners and the fans breathing down their necks, whilst trying not to repeat themselves or paint themselves into corners.
The next game will, of course, expand on some of these stories, retcon others, and ignore some entirely, the same way MKX did with MK9 or many movie and comic series do. I *certainly* don't think more chapters are coming as DLC.
I enjoyed the story, but, like many others, I preferred MK9s by far.
The voice acting and motion capture in X were a step up though and It was still head and shoulders, over any other fighting game efforts.
Ive always approached MK lore exactly like comic book lore: Everything only matters in the moment, death means dick, nothings set in stone and, crucially, just because something happened doesn't mean you'll ever get clarification on why, or that it won't be completely ignored later.
Decisions are made around the table, years after the fact, with a 50/50 balance between "what's good for story" and "what's good for sales"
Mileena will be in the next game, Shang Tsung will come back, Scorpion will become demonised again and at least two of the new characters will likely not be on the roster. Hell, somewhere down the line we'll see Sektor/Cyrax/Jade again.
Because Mortal Kombat is a world of souls and magic, necromancy and resurrection, realms and gods, all supported by passionate, and occasionally obsessive, fans. In that kind of world, you can have *anything* happen in the blink of a narrative eye.
I guess it's one of the reasons we love it.
But still, *Princess* Kitana in charge instead of *Queen* Sindel? Really?
Ninja, please...