When you have a cast and a story as wide spreading as the Mortal Kombat franchise, there is a good chance you're going to over complicate things. This is the real problem with how big the Armageddon Roster was. They don't learn their lessons, of course, and upon rebooting the franchise, there was now a more solid, smaller cast of main characters, but that doesn't stop them from pouring more and more of the action figures onto the play area. Now, there are playable characters and partially playable characters everywhere you look. Let's just hit you with the SPOILER ALERT for this whole thing on the MK Lore as a whole.
Mortal Kombat 9 brought about a new cast of characters, mostly made up of old and returning characters already existing in the franchise. This was an understandable change across the board, but of course, there was more killing characters and attempting to bring in new ones for a new generation of games. This was why MKX suffered storywise. They wanted to put the Cage family up on the highest bar of the cast, but they just went about it in a clumsy way. Now Cassie Cage isn't even in MK1.
Kitana
The worst way they handled the new generation turned out to be the best way in the end. And no, we're not including the Shang Tsung alternate ending. Kitana started out as the unwitting pawn in Shao Khan's games. It turned out he did not care about her and she became quite the sympathetic character as she struggles in the fight to the survive. In the mean time, she not only gains a love interest, Liu Kang, but also a "sister". Mileena became her clone, or they just stuck with sister and true daughter of Shao Kahn. She learns about all of the lies he told her about their family and relationship, and then she ends up getting killed by her mother. Yes, all of that happened in MK9.
They bring her back to life, of course, but what they do after bringing her back in the time conversion of MK11. Now she is back and so is her lineage. Mileena has been killed in this timeline (another reason to hate D'Vorah), so once Kitana kills Shao Kahn (in this timeline, not in the Shang Tsung DLC), she becomes Kitana Kahn. This was one direction that actually works, aside from the arguments online. Seriously, she has been seen to be a great character and morally in the green while killing her opponents. The fact that Liu Kang chooses to spend eternity with her once he becomes the God of Fire and Thunder is just a very good ending for that particular timeline. This was the high note they should have ended it with, but of course additional entries have retconned and stomped on this part, but it was a nice touch.
Frost
As Sub-Zero himself said, "Wasted Potential". This was a character that could have been treated a lot better. Bringing her back as a mostly robot with a detachable human head would not have been on the top tier as far as ideas go. This was a potential character that could have gone against Kuai Liang and then learned that his defeats of her were training her and helping her learn how to fight. Instead, they turned her crazy, made her get a robot body and KILL the entire Lin Kuei in order to make a robot army. This could have been a new female Sub-Zero character who earned her way to that title, if Kuai ever decided to pass the mantle. It's alright to make her a villain, but they really did not need to go this dark with her story.
Scorpion
Bringing Scorpion back to his humanity was one of the best touches they could bring to the character. At the same time, it wasn't such a terrible thing to go back to the Classic Scorpion at the end of MK11 either. It's a conundrum as far as this character goes. Having Sensei Hanzo Hasashi team up with Master Kuai Liang was a touch of brilliance. Their relationship has been very hard, considering it was Scorpion who killed Bi Han and created Noob Saibot as a result.
Now, having him killed by D'Vorah was a stroke of stupid. He could have gone out like a champion, but they gave him to the character that they apparently want to promote in some way. What they did was piss off the fanbase. The way a character dies matters a lot, and yes they had the replacement for him on hand, but come on! It's good that they didn't go the Mortal Kombat 3 way and leave out Scorpion in any way.
Raiden
In the end, Raiden is a very complicated matter. For some reason, in the Mortal Kombat franchise, he either have his powers in Outworld or he doesn't do crap. Either the gods can't intervene or he can just go wild and kill things with abandon. Seriously, the way the plot treats Raiden can mean a lot of quality points when it comes to Mortal Kombat. Thankfully, MK9 and up throw away his leash and allow him to do a lot of stuff, including resetting the entire universe in order to get back to the basics.
Then, for some reason, the story decided to turn him evil. Well, semi-evil, if I'm being truthful. He's still fighting the evil people and killing them before they can invade, but still, he's overusing his power here and any elder god of old would have gotten involved by that point. Still, it's nice to know that the door swings both ways. Shao Kahn abused the rules of Mortal Kombat, so Raiden can teleport into their realm and destroy them with his thunder and lightning.
There are mixed feelings about giving all of his powers to Liu Kang in the end. Hell, there's a lot of mixed feelings about him killing Liu Kang in MK9. That's why the way they did it was something of a stroke of genius, story wise. The build up between the two of them as two beings who handle situations differently, to fighting each other endlessly, it had a very nice flow to it when Raiden decides to end it all by joining forces with Liu Kang as the God of Thunder and Fire. It's a long way to jump, but they handled it rather well over all. It was nice that Raiden got his true happy ending when he talked to Liu Kang by the end of it, saying he was proud to be mortal again. This was where his character should have stopped, but of course, you get the idea where the series needs to go from there.
Cyber Sub-Zero
Now, stay with me on this one. We should at least be thankful we had this character made a reality. They were able to kill him and bring him back to life, of course, as we only see Revenant Sub-Zero at the beginning of MKX. From there, we can deduce that he was among the resurrected. Still, it was cool to have the cybernetic version. It's just a shame we never got to see Smoke very much at all in this part of the franchise. Still, Cyber Sub-Zero remains an oddity in the series, and that's really a shame. His cybernetic ice moves were awesome and just the thought of him going through the Cyber Initiative and then being able to remember it is just a nightmarish thought. It was good to have Kuai Liang back, though, and having him be the head of the Lin Kuei was kind of a no-brainer. So good on that.
Shao Kahn
In the beginning, Shao Kahn was the highest level of god tier when it came to villains in the Mortal Kombat lore. Of course, then they came up with Shinnok and Quan Chi just in time for MK4. Quan Chi wasn't quite as powerful as Shao Kahn, but he was powerful enough to kill him, given the right opportunity. The newer, darker entities were needed, though, because we weren't going to be stuck with Shao Kahn for the entire franchise, we all know this. Still, how they brought about his final end was divisive. However, I would prefer his face getting cut off by Kitana over all of the garbage storytelling that they contrived for the Shang Tsung alternate ending.
The real problem with Shao Kahn is that they kept him around being a playable character, but they just kept weakening him throughout the story mode. People end up defeating him on such a regular basis, he just loses so much of his overpowering charm from his original days. It used to be an achievement to defeat Shao Kahn, but now they just bring him about in order to have a slightly more threatening antagonist. Taking him down in the power scale was a decision that killed Shao Kahn's reputation, making him weaker and more vulnerable. Killing him off in an epic and story-driven way would be preferable to this treatment. Perhaps, if they decide to make him a main antagonist for a final time, they can give him a properly awesome ending. Otherwise, just let him go.
There are so many characters in the Mortal Kombat franchise and not all of them can be given the proper attention. This is a very large problem when they decide to jumble up their roster. That's not even to mention the special guest characters: Alien, Freddy, Leatherface, Terminator, Robocop, Spawn and more! Look, I would appreciate these characters a lot more if they didn't bring in so many characters and screwing up their power ranking. MKX was torn apart because of the fighters that defeated people supposedly three times their own power. The story becomes a mess when you decide to toss your continuity out the window. Just because you include these characters into the roster does not mean you need to shove them all AND MORE into the story. This is especially true when those additional characters are just paid DLC. Stories need focus and the more you toss to the wayside, the more the story gets pushback. Defend Earthrealm and be ready for what comes next!