After Completing the full game this morning, I can whole heartedly say this is the absolute best MK Story in the current trilogy and the second best story in the entire series right below Deception.
I'll get the cons out of the way since they're easier to point out. One is the major flaw I stated 2 pages ago, but thankfully that was the only one. They really have left far too much stuff out of the story in terms of characters who should be there. While I'm glad they actually addressed the fates of every character I wondered about, truth be told a lot of the reasonings were crappy. And while people question how Frost could defeat Fujin, you all must have forgotten that only she and Subzero truly stand a chance against gods like Fujin as stated in MKMSZ due to their mastery of cryomancy. They really shouldn't restricted these important pieces of information to intro dialogues. Even a lengthy text-based synopsis in the Kollection of everything that happened between MKX and MK11 would've worked fine, but not in intro dialogue that most people might skip. I'm not counting anything from the krypt as canon due to the fact that every death there conflicts with the actual story of all three games so I'm not worrying about that. The ending portion of the game was great, but I really feel they should cut everything but the Cetrion and Kronika fight out of it and just end the fight with the revenants through the cutscene. As for scorpion's death, I felt somewhat emotional not gonna lie. After the honeymoon period for that I remembered something that makes no sense for the writer of the MKX comic to forget: Hanzo died in the comics and came back to life due to Scorpion. He is should in the actual cutscene during his fight with scorpion that he still has his powers. So why couldn't he just come back to life after a while instead of it being just Scorpion from the past taking over? The ending was also kinda flat. I liked that they had a bad ending, but they could've done better with the other two endings. So far, MK9 definitely has the best ending in the series with Shaolin Monks having the second best ending. The last issue is that, as with MKX, there are many portions of the story that could've been tag or handicap fights, yet they still refuse to bring those back.
The pros, they reused characters for other chapters. Specifically:
They reduce the number of Jobbers to 3 (Geras, Kabal, and Noob Saibot) and gave others an actual role. Most would argue that Erron Black, the Kollector, and Frost were jobbers in this game, but they actually have roles and motivations that are important to the story outside of just being someone to fight. In detail:
As stated before, they actually address EVERYTHING, including the fact that Cassie beat Shinnok. The brag about how someone like Cassie was able to defeat Shinnok, but they also acknowledge the fact that without the Halo power a**pull she never would've beaten him, thus removing all questions about how strong she is as the halo only seems to work on gods and only under certain conditions. Hell, even Lui Kang needed an a**pull to beat Kronika, though that was much more believable to an extent.
The absolute greatest part of the story mode was Raiden's chapter. Not gonna even go on an extended explanation of it. I absolutely loved it from the story, to the characters, to the pacing. And the transition from chapter 10 to chapter 11 was seamless. The way the shot the plot twist reminded me a lot of the fight between Kakashi and Obito and the final fight between Sasuke and Naruto where they paralleled the action between the past and present.
Overall, this story mode will be replayed sometime in the near future because I loved it that much.