Leutin09 made a video on the "5 biggest problems in 40klore, that can never be fixed"
To give a brief summary of the video:
Introduction:
40k exists as thsi weird setting where rather than having a tabletop game inspired/based on an existing property with a set story and advancing timeline, it's instead the reverse, with lore being beholden to the tabletop: the lore can't advance because it needs to support yearly releases for the tabletop game, but also since 8th edition with the return of Guilliman, it still appears to have set an actual plot with main characters and "main story", but it still advances at a glacial pace because, again, beholden to the limitations of a tabletop game. (he notes that we're already two years after the Lion's return, but that beyond the Arks of Omen narrative, Lionel hasn't really done anything). Unfortunately, the fact that the lore is advancing now means that a lot of "this will be the end of the setting... at some point" plot hooks are left dangling, left in a state of "should result in a climactic fight, but needs to resolved in a way that leave the tabletop game existing as is".
Problem 1 and 2: The Tyranid and Necrons levels of power
Both are the same problem of "every single bit of lore about these factions told us they "will destroy the galaxy if they're at full power, and they are getting there Soon™". With the Tyranid it was "when the full might of the Hive Mind arrives", for the Necrosn it was "when they all wake up"
Well, the Hive Mind is there now (it's nominally the focus of 10th edition) and the Silent King is back (was in the trailers for 9th edition) and... nothing, really.
The Silent King's plot has fizzled out and stalled in the Pariah Nexus, and the Hive Mind's greant assault happened... two years ago and hasn't doen anything since.
But with how much build up there was about "the eventual full might of these will happen", you can't really have them just be "well they're just another minor faction amongst them all" without it feeling like an absolute cop-out.
Lueting's idea to "solve" these two problems is that the Tyranid's connection to the Hive Mind can be severed, making it possible to have "Splinter fleet". Each mighty and dangerous, but it would bring their levels of power down to a level where it wouldn't feel too weird that they don't just roflstomp everything.
His idea to solve the Necrons problem is what GW seems to already be doing for the Pariah nexus: there are some of their mightiest weapons that even the necrons themselves don't want to use, and there is a civil war because not everyone obeys the Silent King.
Problem 3: The Return of the Primarchs
Roboute coming back was momentous, setting-altering, once-in-a-lifetime event. But GW will doubtlessly bring back more Primarchs (to sell their minis), so each time a Primarch return, it feels less special. It also shrinks the setting to "another family drama", where you know the main characters are too special to ever have anything meaningful happen to them, because they would never get removed from the setting. It diminish the sense of loss and tragedy and "great past that's fully gone" that was key to the Imperium's theming, and each resurrection feels less and less special and noteworthy (see how many "when is Primarch X coming back" posts here, at this point the primarchs all returning doesn't feel special, because everyone expects them all to return)
Luetin's idea to solve this: have a hard cap to the number of primarchs that return, hard confirming some of them as truly dead. Not just "dead (but will return anytime GW wants to)", but as outright forever gone.
Problem 4: In the Imperium vs Chaos conflict, neither can win or lose
Chaos can't win because that would involve destroying the Imperium for good, but the Imperium can't destroy Chaos either because once they do that... well they can just destroy everyone else (and also the setting is over). Which means that for all the Indomitus Crusade is supposed to do, it can't ever really bring order back fully, and for all the Black Crusade are mighty warhosts with the ultimate goal of destroying/conquering terra, they can't do that either, making it all to a perpetual stalemate that makes Chaos look less impressive as bad guy.
Luetin's solution: emphasize more the internal struggle of the Imperium, and give chaos more down-to-earth goals and more humane elements. Shift things so chaos has a mini-empire in the galaxy, so they can have more focused stories that don't need to end with the imperium's total destruction to be satisfying and focus more on the mental/moral corruption by chaos, rather always involve military mights.
Problem 5: The Emperor is too powerful but too faillible
To keep it short, the Emperor ping-pongs between "nearly omniscient figure that could predict things centuries, if not millenia in advance" and "powerful psyker, but ultimately just human". And while Luetin understands that it's the point of the character, he feels like there should have been more hints at his nature and characterisation, rather than being kept so deliberately vague that we ultimately can't really say anything about him.
Luetin ends the video by saying that he understand all those are "necessary" to provide plot hooks, invite speculations, and provide a tabletop experience where X can fight Y for any number of reasons and could reasonably win or lose without feeling too weird, so he understands the pure "gameplay" reasoning behind these problems, (and they're probably not even really problems from GW's perpective), but it does ultimately hamper 40k as a setting.