1. Mileena is now the new ruler of Outworld with both Tsung and Kahn dead. Shinnok and Quan Chi will try to take the realm from her. Keep in mind that her only real reasons to join Shinnok in the original story was because she was killed by Kitana and reborn in the Netherrealm. That didn't happen this time around, of course. Raiden, still changing events to ensure Armageddon's prevention, will take this as an opportunity to convince Mileena to join Earthrealm's
side and repel Shinnok's invasions.
2. Of course, Shinnok and his legions of darkness will escape the Netherrealm and begin their quests to rule all of the realms.
3. With the Netherrealm a deadly threat now, Earthrealm and Outworld may have to join forces to stop Shinnok. Reptile, in particular, may become a force for good should Raiden inform him about what really happened to his race. Shao Kahn did kill off the rest of his race, but Shinnok and his war with Raiden, which took place in Earthrealm, basically killed off the majority of the Saurian race. Like with Scorpion and his dead clan, Raiden could make a deal with Reptile that he will ask the Elder Gods to bring his race back from the abyss should he help protect Earthrealm.
4. Rain's backstory, goals in life, and ultimate role in the series will be revealed (good or evil).
5. Tanya will be a major villain again, like last time.
6. Shinnok could find out about Quan Chi keeping his amulet instead of giving it to him.
6. Johnny Cage will be the one to defeat Shinnok. However, Raiden could take him to Seido, the realm of Order, to train him to become a warrior powerful enough to defeat Shinnok, like in his ending.
7. Sub-Zero's MK4 ending, instead of Scorpion's MK4 ending, will happen this time around, including Scorpion killing Quan Chi. Thus, no Deadly Alliance.
8. The war against Shinnok will be longer and more epic this time around.
9. Liu Kang is not under Quan Chi's control, may not be dead even, but he won't be the one to defeat Shinnok. He will rebel against Raiden if he is not dead or revived by the Elder Gods; in fact, he may be swayed to fight for Shinnok; Shinnok could lie to him and tell him he is an Elder God fighting for a greater cause. He could also use his disappointment in Raiden as bait, and tell him that the dead Earthrealm warriors (including Kitana) have already been resurrected and "joined" Shinnok's side, which would ultimately sway him to Shinnok's side.