They said she want to reset time, not go back to the old timeline. To me, they are saying they wanna rewind back to the beginning of time, start EVERYTHING again.
Now, they literally stated they're doing that just for Shinnok. Not exactly for him, but because he was key figure into something we don't know yet. I disagree Shao Kahn was a better leader, I think they were different kinds of leaders. Kahn was a ruthless, all powerful dictator that ruled out of fear, and people respected him due fear. Shinnok's loyalty is a little deeper: they fight for him because they believe in what he believes.
Now that's the question: what does Shinnok believe? They never went deep into that. It was only in MKX that they revealed he did not want to rule Earthrealm, but to poison and kill all life. And in the prologue he mentions Raiden has accepted his truth - of death - and that he cast out not out of pride, but because he mentioned this. We still don't know. Maybe it's something Kronika agrees. Maybe Shinnok has a view on life that she thinks must be the destiny of all life, and Raiden took out the only one that believes in that. Maybe he's right, maybe everything must die. She was probably respecting rules as the Elder Gods - and even Raiden - used to, but enough is enough.
Another thing: Shao Kahn and Shinnok are totally different elements into the Armageddon lore. The Armageddon is (1)kombatants growing so numerous and too powerful that they would tap into the forces that make the realms balanced and lead to its destruction; (2) Shinnok didn't invent the Armageddon, but he was the architect by fulfilling the prophecy when he spread the rumor that the Battle of Armageddon had a glorious prize, without him we still have numerous kombatants, we don't have the conflict the way it was, however; (3) Shao Kahn was merely the winner and killer of Earthrealm. If we take Kitana's ending, he was even defeated after killing Earthrealm. In the end Raiden was only protecting our realm.
In other words: Armageddon = cars/ Shinnok = Enzo Ferrari/ Shao Kahn = Michael Schumacher. Schumacher is unfortunately not a pilot anymore, but Ferrari lives on. Here, someone made something that took Ferrari out, despite having F1 cars of other genres. So, someone wants to put Ferrari back, not exactly to make Schumacher win, but for some reason we still don't know.
I... said in the very first sentence. "LITERALLY EVERYTHING" myself.
To be honest it is kinda pointless to even argue about this. Because this story has no consistency.
You're writing like everything was planned from the beginning. The story is being made with every new game. They didn't "reveal" shit about Shinnok.
MK4 Shinnok wanted revenge against Raiden for imprisoning him.
MKA Shinnok wasn't even planning the armageddon. He was as blown away by this shit, as everyone else. He just wanted the power on top of the pyramid of Argus. He wanted to rule supreme. Simple. It was cut and clear back in the day. NOW they are trying to make this complicated.
MKX simply CHANGED his goal, to killing all life and shit.
This entire thing with Kronika is nothing more, but a cheap PR stunt, that was done as a "last second thing." (Game franchise wise)
"She was behind everything!" Sounds good, IF MK lore was deep enough for that.
Not in a single Original MK game it was even mentioned that Shinnok was the key to anything or has some sort of hidden agenda. He was literally just another power hungry villain.
So yeah. What they are trying to sell here, only applies to Rebooted universe. Not the original. In Original timeline, the battle of Armageddon happened not, because Shinnok was fullfiling the Prophecy. Prophecy was actually for Daegon and Taven only. That whole pyramid was just for them. But Shinnok wanted the power, so he alerted other kombatants, so they would get in the way of Daegon or Taven (as pyramid only appeared if one of them died). His plan was for all kombatants to kill each other, while he would walk past everyone and get his prize. And his prize was clear. Rule Supreme. Not awaken One Being. Because...
This entire thing with One Being being ressurected started only in Rebooted universe. In Original timeline, One Being only stood for a legend about 6 Kamidogu and a Sacred Amulet that would grant insane power. Those 6 Kamidogu were actually rebooted in MKX as daggers.
In short... Story wise and how the story has flown Shinnok is nowhere even close to being special. But once again. MK never had any consistency so if they decided to claim that Kronika is taking special care of Shinnok (though never seen a claim like that, I only seen claims that could be easily understood as Shinnok being the last straw for Kronika, not some sort of key player) then... ok.
But that just proves my point again. If you don't have a set lore, you get shit like this. They already changed a lot of things from original MK, so this entire "Kronika was behind everything" is the same as revealing Joker's name and origins in DC Comics. Yeah cool. His name is John and he had a wife, but if I go 5 series back, I can show you, that you're full of shit. Same with MK.
So in the end of the day. Let's agree to disagree on everything.
EDIT: Actually there was this one guy trying to pull shit like this with Captain America. Made him into a sleeper Hydra Agent. Writer even tried to defend that shit, by saying that if you look closely in the beginning of Captain America series, you can see the signs. Pretty fast, people showed him that he was full of shit, and Marvel went with "it was an alternate Captain Rogers" road to fix the mess.