I don't really get everyone's problems with Flux, personally. Was it perfect? No, but I've watched it twice now along with the prior seasons and it feels at least on par.
It's a pretty significant drop in quality, I was enjoying myself until I got to Flux, even though there was a clear drop it the quality of the writing before it. It spends so much time trying to build a mystery but doesn't give enough information to really make it intriguing for me, then it just solves whatever that was over the course of a few minutes and skips over to another.
Flux is poorly written throughout and it destroys everything we know about the doctor. Previously the doctor was basically a rogue escapee of a morally ambiguous and very powerful alien race, but now is instead the entire reason for that race's existence. Powerful, immortal, and with a past we now know practically nothing about...it completely changed the dynamic of the show and retconned the doctor's entire backstory just for a cheap surprise that goes completely against everything we knew, and they didn't even manage to deliver it well. May as well make the doctor "the chosen one."
*Preemptive apologies for the wall-o-text. I honestly tried to keep it brief.
then it just solves whatever that was over the course of a few minutes and skips over to another.
It was definitely briskly paced, but I didn't feel like that made it awful. It's also worth keeping in mind that the series was made around the start of the pandemic with some pretty big restrictions. That doesn't mean it's automatically good, of course, but I feel it deserves a bit of a break for imperfections.
it completely changed the dynamic of the show and retconned the doctor's entire backstory
I guess I just don't see it that way. Change is inevitable if a show wants to keep going, and mystery is what keeps most people engaged. "What does it mean?!", "What will this lead to next!?", etc. Whether that's delivered well is up to opinion, I suppose, but I don't think Flux utterly dropped the ball there.
In regards to The Doctor's importance to the universe, they've kind of always been a not-so-directly-called-out "chosen one". I think Moffat was the most brazen with that angle, tbh. Not Chibnal.
And has "The Doctor started the Timelords" plot twist not been screaming out to everyone else for forever already? Personally I thought they would end up revealed to be half-human at some point, too, so this felt pretty mild to me in regards to "completely changing the dynamic of the show".
I dunno. I just don't see what is apparently super obvious to everyone else. It felt like pretty standard Dr Who to me and all the grousing about it feels overdone and amplified by others that are more upset about the other changes that 13 brought to the show, that the whole arc felt tainted by, which sucks. (To be clear, I'm not saying that's what you're complaining about, just that it's an ever-present shadow on 13's run).
See it didn't feel briskly paced to me, it felt pretty slow because I never knew what was happening up until the end of the episode, then it'd go into high gear for five minutes to setup a cliffhanger, often doing so in a cheap way as well. And what was happening wasn't really interesting. It's a cloud destroying the universe, it's the Nothing from Neverending Story, meh. And the villains seemed like they were taken out of Destiny, yet more noble-ish scifi superbeings.
Maybe it if it was well written I'd like it more, but it's poor and the way characters act is absurd even for Doctor Who. I mean, Yas can just walk onto an alien ship - one she's never seen before - and knows how to use its systems. Nobody reacts to things they should find unbelievable to the point of freaking out beyond a sentence saying "what was that?" These issues pop up in the preceding few seasons, but Flux is just poorly written throughout, so maybe that's why such a massive change is such an issue.
Maybe it's because what was once a rogue timelord skipping about time and space and doing good, having adventures, and saving people is actually another superbeing that is the means through which the timelords were created, an immortal being of incredible power. It just changes the context, well-meaning roguish timelord versus immortal god.
There are brighter spots. I actually liked the dog alien guy, I thought that was going to be bad when it revealed what was going on but I turned out to quite like him. Of course he was paired with John Bishop who I just don't think could pull off the role, which is a shame as I like John Bishop.
In particular - a female Doctor, a black Doctor, a more concerted effort to bring in non-white actors (though still not amazing), etc. The kind of stuff Internet edgelords latch onto and make an issue out of. Again, not wanting to imply that's what you're doing. It's just impossible to ignore for me regarding the overwhelming criticism of that run, which I generally enjoyed.
Back to the writing, though. I don't think any of what you brought up makes it awful or terrible. With the "it's just x from y" critique, all kinds of stories re-use ideas or slap a different name on them. I just see that as how storytelling works. There's not an infinite amount of ways to illustrate everything, so there's pretty much always going to be apparent connections to prior media we've seen. I don't think that makes it bad, just not amazingly innovative.
And in regards to the backstory reveals, I don't really see the character as an "immortal god" anymore than I did before. Immortal ≠ all-powerful, and for all we know, they're just part of some other alien race that's no more (or maybe even less) powerful than Timelords at the height of their power. We just don't know, so it seems a bit premature to jump to "immortal god" when nothing has substantially changed other than some lore. At least in nuWho, The Doctor has always been just-shy of infallible already. Unless they start giving the character comic-book style super powers, I don't really mind it.
I mention the comparisons to other media because that media did it well and Flux didn't. You see the flux a handful of times but in the end it's just something happening on the background whilst these immensely unoriginal and boring supervillains wander around being similarly uninteresting. Even on a more basic level, it's yet another antagonist destroying the entire universe. Doctor gets between universes again, just gets jerked around constantly and only ever reacting to things because even she doesn't know what is happening. And people get teleported around constantly, often as the means it escape from danger which is unspeakably cheap, a man who has barely seen a lightbulb steps inside the TARDIS and is only mildly surprised by how completely impossible everything he's seeing is. Episode ending cliffhangers not resolved but subverted within a minute of the beginning of the next episode.
In what world is it too early to "jump" to immortal god, considering that's basically what they said in the show? Thousands of lives, she doesn't die she regenerates indefinitely forever. She IS immortal and that's the power of a god. Previously there have been references to the doctor appearing godlike due to the basically magic-seeming TARDIS, her tech, being benevolent, helping out everywhere and then disappearing. Well now it's not a naive, yet charming notion from a lifeform that's not advanced enough to understand. She IS one. She is no longer the roguish timelord objector going on adventures, which is the dynamic I liked.
Future huge story reveals will be about her past, and it'll just be unknowable, impossible to empathise with things like "oh it turns out I'm an ancient god" or "it turns out I'm the last of a different and even more powerful race now" which I think would actually be worse, imagine wading through all this shite just for it to basically be the same as before.
I like the traveller encountering problems and fixing them setup, I don't really like the "person showing up to a random problem happens to be the most important person that's related to that problem and also in the universe" really, especially when she's a god. You say you won't mind unless the doctor gets superpowers, but I wouldn't be surprised if something similar turned up. I bet there's a thing the doctor will have to do because they're a powerful ancient race, the only that race could withstand it.
On the other hand I didn't hate the Christmas special, so we will see. At least the butcher that wrote the flux is gone.