I have my theories on the story.
Fair warning: wall of text.
We have some very clear parallels between both timelines, which, as of MK11, we now know both exist (because due Kronika saying that Raiden screws things up, she can see the original timeline and now the new one) separately of each other.
Parallels:
Liu Kang dies: OTL by the deadly alliance. NTL by Raiden.
Scorpion is resurrected: OTL by the Elder Gods as their champion (Deception). NTL by reversing QC's magic and restoring him to life as Hanzo again.
Raiden becomes Dark Raiden: OTL his ending in Deception. NTL At the end of MKX.
Ok, these are 3 pretty big parallels between the old time line and new one. So, if this rings true, then it is quite possible that no matter what, Armageddon is coming, regardless of the way we get there. No matter how much Raiden interfered and attempted to change anything, those 3 things are all going to happen, which are all leading to Armageddon.
Now, since we know that Kronika has been controlling everything since the beginning of time, it means that Armageddon is/was her plan. This also means that in the context of the story, Kronika is AWARE that the events of MK4, MKDA, MKD and MKA all took place at some point, and those events are HER intended timeline, which Raiden interferes with.
This leads to some questions:
1. Blaze is actually the final boss at the end of Armageddon, does this mean that, by MK9's storytelling, Shao Kahn defeats and kills Raiden for the right to fight Blaze? What is the outcome of that fight, and, is this SK the one that we will get to see in MK11?
2. Will Blaze be featured in MK11 since all roads are seemingly leading to Armageddon, and if so, what is his role? If not, then what character is?
3. If Kronika is the one controlling everything behind the scenes, including the action/non-action of the elder gods, that makes her more powerful than the Elder Gods. Is she actually the one-being? If she is, then that is further proof of the existence of the Kamidogu, and moreso, Shujinko's existence, and likewise, the possibility of Onaga's existence in this timeline.
4. Is Kronika benevoltent or malevolent?
5. This is a food for thought observation/question. Are the Elder Gods actually Malevolent beings? They choose to act and not act when it is clear that they need to act. Shinnok sheds his EG status, and eventually so does Raiden (Raiden's defection is due to the EG's lack of direct action). We are led to believe that Shinnok is evil, and likewise that Dark Raiden is evil, but in the MK11 storyline teaser, we see Shinnok telling Raiden that he now sees the "truth" about the Elder Gods, seeing as they have both gone from EG status to "evil in our eyes" status. What if the truth is that the Elder Gods are actually malevolent, and Shinnok, Dark Raiden and Kronika are all actually neutral or good?