Some of the things you've said do have answers to them. Like why she doesn't kill them immediately. She knows some of the Earthrealmers need to survive for her vision of the timeline to play out perfectly.
She's a psychopath at the end of the day. The hourglass is her play thing. She just wants to have it all done her way and she'll string along as many people as she needs to, to get that done.
But rather than respond to all your criticism (a decent amount of which, is pretty valid). I'll just say that as far as these little 4 hour stories go, especially ones which have been retconned as many times as MK has, I tend to just fill in the gaps with whatever I think could've happened and it makes me happy enough to enjoy it.
Switch off my brain, play the game and when a question pops up (and good God, do I have questions about this story), just fill in the gaps myself till Im ok with it.
Overall, yea, it does seem like MKX's story was basically pointless other than the death of Shinnok and setting up Dark Raiden. And while the dialogue and nitty gritties of MK11 leave quite a lot to be desired, I can't say I'm totally unhappy with the plot.
I LOVE how they took the time to treat Jax like an actual person and build his character. Give him actual motivations for joining Kronika even if he really didnt want to.
I really like where they took Raiden's arc. You say that these visions came from nowhere, but I see it as the final culmination of the visions MK Armageddon/MK9 Raiden was trying to send to his past self. Like, after all these years and all these timelines, he finally fucking gets it. He finally sent the right visions across. He finally understands. And it all clicks in place.
The juxtaposition between Nether Liu and Kitana vs. Time Lord Liu and Kitana was pretty neat as well. That they, from personal experience, know just how bad the lives of individuals could end up if their destinies are played with. And that they in the end, get to craft a world where people may not have to suffer that fate. That Raiden took the time to assess how bad he fucked up and that he maybe wasn't deserving of his title of protector of Earthrealm. And that he could transfer his power to someone else more worthy.
This is in direct contrast to Revenant Kung Lao who is resentful and angry (much like Raiden was becoming) that Liu was the chosen one. He says it in the story "It should've always been me." But Raiden is able to get over it and help the true chosen one by pushing his power beyond what it was before.
And the story gameplay as well, we got to see so much of the universe. Rather than constantly coming back to one location, everyone was everywhere doing different things. Yea, they could've spent more time delving deeper into it, but I dunno, I saw you don't like the FG excuse, but... FG game. We were never going to get a 20 hour story mode.
All I'm saying is if you bulletpoint the story and not focus on those annoying nitty gritties, this story was actually hella enjoyable and kinda surprising and bold and took way more time to flesh out it's characters at the very least, if not the plot in its entirety.