I'm sure that this was not NRS's intention, nor do I think this will be addressed in MK11 or any other game in the future. And honestly, I'm a little too old to care about the canonical inconsistencies of the franchise, I just enjoy the new timeline for what it is.

However, that being said, I do have a potential, arguably far fetched, theory about these inconsistencies. My theory is that somehow, Quan Chi was aware of the original timeline in MK9, and maybe even prior to MK9. He's far more active as a character during the events of MK9 than he was in the original timeline (where he didn't even exist as a character in the original trilogy, obviously). So what if somehow, he either sent a similar vision of the timeline to himself prior to dying during Armageddon, or somehow, his soul piggybacked onto Raiden's vision (maybe because he was killed close to the pyramid's apex and his spirit lingered). Either way, maybe Quan Chi was privy to how things turned out in the original timeline, and as a result, manages to change things even further to manipulate things to his advantage.

The reason why I sometimes entertain this theory is because not only does Quan Chi always seem like he's in total control of the situation, and nothing about the circumstances surprises him, but it would explain why he's constantly undermining Shang Tsung by appeasing Shao Kahn in order to gain his favor, right down to stealing the idea of resurrecting Sindel before Shang Tsung could even think of it.

The end result is that Earthrealm loses most of its fighters, including Liu Kang, who was Earth's champion in the previous timeline. Not only this, but it allows him to enslave these fallen warriors as Revenants, and seemingly tip the balance of power in Shinnok's favor, even though in the end, Earthrealm still managed to win the war.

That's the other thing, his motivations don't exactly stay consistent with the original timeline. He no longer seems interested in betraying Shinnok to usurp all the power for himself. Maybe he saw the result of his actions from the original timeline, and how he ended up being trapped in the Netherrealm for years, to be tortured by Scorpion, and then later, being killed by Raiden's suicide blast, and, of course, then in the end, meeting his fate near the Pyramid's apex during the Armageddon battle. And seeing all this, maybe he decided that it was in his best interests to remain loyal to Shinnok, and take his chances being on good terms with the elder god.

Considering how drastically the second timeline ends up being altered during the events of MKX, and the fact that its main plot seems to be taking place later, chronologically, than Armageddon would have, this could also explain why in MKX, Quan Chi has to play things by ear, and no longer seems like the all-knowing manipulator of the events around him.

There are a lot of other things about MK9 that didn't line up at the beginning of Shang Tsung's tournament, such as the presence of Nightwolf, Sektor and Cyrax, as well as many more of Outworld's warriors, such as Baraka, Sheeva, and Ermac. That's also why I entertained the idea that maybe Quan Chi was aware of the original timeline even before Raiden was, and maybe something he did prior to the tournament either caused a butterfly effect which led to more of these characters being there, or it was something that Quan Chi foresaw as being advantageous to him, and as a result, manipulated the events to ensure that all those warriors would be present during the first tournament. Setting up his chess pieces, so to speak.

So yeah, that's my little theory. Like I said, I don't expect it to be considered canon ever, and NRS will likely never revisit the subject... Or maybe they'll disprove it completely in MK11. But yeah, for the past few years, it's just something I considered in my own mind, to potentially explain why there are so many inconsistencies right from the beginning of the new timeline. I just wanted to share it.