Well, after much thinking and contemplationg...I have come up with the following theories and posibilities.

Quan Chi in MKD
If you look in Quan Chi's level in MK:DA he has the same bug/spider symbol that the level in MK:D has and also resembles the weapon andsame red ruby on it. There is either something really big that happens in this level or Quan Chi is in MK:D. If not then I can also see him and Shang being destroyed by each other or earthrealm fighters or maybe even the Dragon King himself?

Ermac and Kenshi
Well, I recall somewhere in Konquest mode Kenshi learned his telenetic abilities from Ermac. These two may have a past somewhere in MK. There can be a lot of deception to go with these two for sure.

The Dragon King
He has been mentioned to be very deceptive. He must play a huge role in MK:D, and may be the reason for all the classics to come back for one more chance. I can see a huge teaming up of forces containing some good and evil fighters working together to defeat the Dragon King and his army of the dead.

Shang Stung
I am betting he will not take part in this game as a playable character. He may be in the storyline, but I think he has been decieved by Quan Chi. He will most likely die.

Reptile
He is mentioned to be the Sub Boss in MK:D. I do not have any problems seeing him as a more evil and now even more de-evolved down to a dragon type monster.

Kira
She is a new Red Dragon member, but she may just be someone we have known from the beginning. As the main plot is deception, it can be our beloved Sonya in desguise to fool the Red Dragon members into going right into a trap.

Skab
He may have a new name, but he looks to me like he could be Reiko. He has the same costume and looks as Reiko, but now he has a burnt face. They're can be many explanations for this, but I am going with my theory of him being cursed by Shao Kahn's mask. He will continue to die slowly and the most painful death as punishment for touching Shao Kahn's mask.

Smoke
He looks as if he is coming back as a human, but I do not dought his 2nd costume will be his former robotic form. He is most likely back because of Sub-Zero recruiting new Lin Kuei members. He is now fighting on the force for good back with his friend Sub-Zero. He may decieve Sub-Zero, but we will have to see about that.

I think MK:D is going to be one big ass war with many different sides. (Shao Kahn) (Dragon King) (Good Guys)

Feedback.

And, if you have a theory, feel free to add it.