My Thoughts:
Shang and Quan Chi thought they had killed Shao Kahn, but in fact did not. All we saw was a bloody helmet. Lui Kang still was killed off by Shang as we all saw.
Raiden has gone off the edge a bit because he thought Lui Kang was the chosen one, and now he is dead. Raiden can't see into the future and is very uncertain about who the chosen one will be.
Shao Kahn somehow faked his death, for he knew the dragon king would be ressurected someday. Once this took place, he would step in and somehow control him. To take Earth Realm once and for all. He will get close to achieving his goal, but somehow, some way, the "chosen one" will stop him.
As far as Shang Tsung and Quan Chi's fate, one of them will die. I believe Shang will again come out like a snake and Quan Chi will finally see his end. Either Scorpian or somebody else will end his life.
Some of the characters will parish in this game for good. I think most of the ninja's and one or two main characters will buy the farm when it's all over.
I think Baraka will have an impact on the storyline somehow. I have this feeling...

THose are my thoughts.