1. Detached Warp Nacelles
Dumbest idea in history.
Saru mentioned that it improved maneuverability at impulse... which on one hand makes sense if you consider the premise the nacelles are the heaviest part of a starship, HOWEVER, on the other hand, it doesn't make ANY sense because SF ships already achieved exceedingly high maneuverability at sublight by reducing their inertial mass via establishing a low level subspace field around them (which results in really high sublight velocities of at least 75 000 km per second and maneuverability comparable to small fighter craft) - which is what SF has been doing since at least 23rd and 24th centuries (field control) - heck, the USS Discovery itself showed greater maneuverability in Season 1 at sublight than it did in the 32nd century.
To me field manipulation (aka inertial mass reduction via subspace fields) seems more efficient.
The writers may have forgotten about this or just wanted something 'cool' to add so as to make ships more visually different.
I would have to say though that WIFI power transfer exists in 24th century Federation (and in 23rd for that matter), so, having nacelles separate and feeding them more than enough power without losses wouldn't be an issue... in fact, perhaps it offers further safety if someone targets the nacelles so they could detach completely from the hull in that case and prevent the damage from spreading to the rest of the ship (albeit this wasn't mentioned).
2. Earth becoming isolationist.
The most unTrek idea in the history of Trek, made worse by the fact that it wasn't rectified by the end of the year.
Perhaps... and their reasons for not being Federation members (self-sustaining) doesn't track. Even before the Burn, I'd imagine that most/all member species planets would have to be self-sufficient to begin with. A space faring society capable of Warp that meets the criteria for joining the Federation would essentially HAVE to be self-sustaining (given what Bajor had to do in order to qualify for Federation membership).
But there was another explanation, they mentioned Earth's safety for why the Federation/SF HQ left Earth in the first place... which from a security point of view does track (since they had no idea who/what caused the Burn and whether it was a targeted attack or not), but in that time, it would have been better that SOL already had built its own Dyson Sphere for example and decided to cut itself off to further for protection - another missed opportunity (that and how they dealt with lack of communications in the episode between Earth and Titan was also ridiculous).
3. Blinking breaking holograms
A flaw from the 23rd century still exists nearly a millennium later? Why didn't Pulaski blink at Moriarty??
I balked at that nonsense too. That 'flaw' would have been eliminated well before late 24th century.
But its possible Kovich introduced these flawed holos specifically for Georgiou... and he was more amused by this premise and could have been testing her. Again, we don't know because nothing was revealed (even as a passing line).
As for why Pulaski didn't blink at Moriarty... probably because she didn't know, and its possible that Moriarty wouldn't be susceptible to this problem seeing how the computer made adjustments so that Moriarty could defeat Data (who in fact WOULD know of this vulnerability in holos... but then, why didn't he TRY it? Maybe he did off-screen briefly - but 24th century holos' didn't have these kinds of vulnerabilities).
I'm not squeamish about it, it's just not right.
It doesn't come out of a "slush tank" the food is materialised from energy, similar to transporter technology.
Exactly.
24th century replicators convert energy into matter... they don't reorganize pre-existing matter into another form of matter (that was what molecular synthesizers did - aka a precursor to replicators). But they are capable of converting matter into energy as well (for recycling purposes mainly - however, for purely new items, they have been stated they convert energy into matter).
However, its possible that SF in the 32nd century decided to use the matter to matter conversion technology instead due to the Burn and overall scarcity that ensued (though to be fair, by the 32nd century, even the non M/AM power sources would be orders of magnitude more powerful than a warp core from the 24th century and energy to matter replicator efficiency would improve to such a degree where it would be literally inconsequential - but, as you know, the writers decided not to progress virtually anything or stick to what was established).
5. The new Turbolift "shafts"
They make literally no sense, what they had before was fine and actually made sense, why change it?
Even Season 1 and 2 both featured huge chasms on Discovery and Enterprise through which turbolifts would move ... but I can see why they would get rid of the support struts for the turbolifts. They were previously maglev based yes, and much like maglev trains require 'tracks' today, they also need those 'tracks' in the 23rd and 24th centuries... now (in the 32nd) they simply decided to get rid of the struts/rails/tracks themselves in order free up internal space and they can do so with programmable matter which materializes things as needed and these things are so finely tuned that they are as reliable as physical matter if not more so. Removing the tracks to free up space makes sense (you can put in more fusion reactors there for example) but without specifically saying that Disco now has TARDIS tech as seen from a previous 30th century time pod ship we saw on ENT... what we saw in the last episode was simply speaking TOO HUGE to fit on the inside of that ship.
6. The reason for the Burn.
So anticlimatic.
Agreed, but to be fair, most things in real life are anticlimatic as well. Most humans tend to make up sensationalist nonsense because they think this is the only way to entertain themselves.
They could have made a reason for the Burn simply speaking different - say it was caused by an extra-galactic species that was close to being a Type IV civilization (and Federation achieving Type III status and starting to transition to Type IV before the Burn and advancing even faster due to how they operate). Classical xenophobia/fear brought into the equation as a reason for attacking the Federation from say half a universe away.
The Spore Drive would literally be invaluable here. The Federation would (realistically) have ability to reach other galaxies fairly effortlessly by this time, but the Spore Drive would be in a different league (as it would be able to go ANYWHERE in the universe... literally) vs say enhanced Warp drive, Coaxial Warp, Transwarp, or even Quantum Slipstream V2 (this one was the fastest, topping out at 10 000 Ly's per minute in the late 24th century).
Although I would have liked to see in that case the Federation moving WAY BEYOND use of dilithium and M/AM in general for power generation by the 32nd century and the more powerful alien race simply having the power of thousands of galaxies at their disposal, whereas the Federation could have had say the Milky Way, Andromeda and a few others in immediate vicinity.