Since we're focusing more on lore than specific narrative and the like...
Fuck it, I'll still go with Naruto and Masashi Kishimoto. I will first note that I have not read Boruto past the first chapter, so any additional fuckery that comes from that, I am not aware of and thus am not factoring into this. Now, many long time readers/viewers are well aware that Naruto's overall story did decline in quality as it went on, but one of the less touched on aspects is how large swathes of series lore as it is first presented is... at best a generous interpretation of what's revealed to be the truth, if not flat out wrong.
Perhaps most emblematic of all this is a simple, basic fact where, if my memory serves me correctly and hasn't been corroded by my general frustration with the series, we're initially told the Third Hokage is supposed to be the strongest Hokage yet. This point is both standard shonen old man badass stuff, but in the particular context of the series, stands as a testament to its idea of how new generations build on what has come before in order to better. It handily also sets a benchmark for what one hopes Naruto will become if he's to ever to exceed the Third as Hokage. This point is summarily reinforced in the Chunin Arc/Sand-Leaf war when, in spite of being decades past his prime, Hiruzen holds off both of his predecessors - brought back from the dead as fucking immortal zombies with infinite chakra - at the same time, and even defeats them, even if at the cost of his own life. The Third Hokage was the strongest hokage, this was a fact of the world.
Except as time went on, Kishimoto fell increasingly into the trap of making older stuff more important, and more powerful. So the First Hokage, who one might previously have imagined was important for being the founder and all, but possibly the weakest of the bunch, turned out to:
A) Have a super special type of tree jutsu so rare that Orochimaru, the initial big bad, tried to replicate it by messing with kids' DNA
B) Have the power to control the Tailed Beasts, which are the most destructive force in the known world. Better yet, he gave them to the other nations as a means of creating a deliberate balance of power
C) Have been so fucking powerful that he was once called the 'God of Shinobi', and this is affirmed with his rival being the only person who could even contest him, said rival basically curbstomping the shit out of everyone when he is brought back as an immortal zombie with infinite chakra.
So that which defined the Third Hokage, and gave us some sense of what the broad progression of the world was meant to be, is undone for the sake of a tired, narrative cliché where the older in time something/someone is, the more powerful it is compared to the present. I could go on - the retcons to the sharingan, the origins of chakra, the outright relationships of the characters prior to when we meet them, etc. Not even the opening scene is left untouched, and while the twist is kinda neat, it's wrapped up in so much other nonsense I think I'd prefer if it had still been, well, the equivalent of a natural disaster as it was initially presented.