I had such high hopes for the story... remember all our amazing theories before the game came out? And what we got was total ass. Literally I at the very least expected something on MK9's level of story, if not better! Again the Injustice comic is so awesome and well written, if they had literally put all the comic as the story, scene for scene, it would have made me a lot happier.
I was so excited for alt universes until it was actually done. I thought there would be loads of earths, but instead we only got 1 (or 0) and 5.
So many opportunities to expand on the story too, I mean half the characters didn't even get their own chapters!