To your first counterpoint; I can see where you're coming from, but the validity of this point hinges on whether the cube was possessed of enough sentience and intelligence to actually adapt in the first place, which I still contend runs contra to what we've seen from the Borg previously.
But since this was specifically and intentionally a situation we haven't encountered before, we can't really definitively say it's inconsistent with what we've seen previously.
I am of the opinion that one should not depart significantly from an established characterisation; if a writer wishes to do so, they must do so in an evolutionary fashion and in a way that makes sense in the universe. I remain unconvinced that this is the case here.
To your second; no, it has not been explicitly stated, as is the case with most Treknology, we must make logical inferences from the information that is available and what we can see on screen. Whether the original Borg concept was backwards or not isn't really at issue, they are an established fictional race with established features, and none of those established features support the concept of sentient cubes.
I think the concept that the Borg have sapient AI is a logical inference from what we've seen, and the concept that they don't is not a logical inference. The Borg have always tended more strongly to the cybernetic than the organic. We know the Queen must be a program rather than a living being, since she re-embodies elsewhere after a given body is destroyed. More broadly, we know that sapient artificial intelligence exists in the Trek universe, we know the Borg have existed long enough and spread far enough that they've surely encountered it before, and we know that the Borg assimilate any technology they find useful.
But what need do the Borg
have for sapient AI? If a component of the Borg is in contact with the Collective, then it does not need to be individually sapient to function, and if it is not, the evidence would suggest that the Borg place within that component a very narrow set of commands and procedures designed solely to re-establish that contact, or failing that, to prevent Borg technology falling into the hands of others.
Further, from what we saw in "Survival Instinct", they have specific protocols in place in order to
avoid autonomy.
For that matter, we have multiple precedents in the Trek universe for even a non-sapient computer spontaneously evolving sentience in the right circumstances: Moriarty, the "Emergence" entity, Voyager's EMH. So even if we stipulate to your premise that a Borg cube's cybernetic systems are, for whatever reason, no more intelligent to start with than a Starfleet computer mainframe, that still doesn't rule out the possibility that they could become self-aware in unusual or extreme circumstances.
Bit this is not how the writer chose to introduce these new "features"; it is strongly implied and, if memory serves, once stated outright that Borg cubes have
always been this way. The writer did not merely create a new scenario, he retroactively applied the results of that scenario to all previous Borg appearances.
Yes, that's exactly the difference. In those cases, the physical technology was massively damaged along with the organic drones, or instead of the organic drones (for instance, in "Collective," the technology was fried but the juvenile drones survived). The technology wasn't just wreckage because the drones died, it was wreckage because the technology itself was physically destroyed, taking the drones with it. This is the opposite case, a circumstance where only the organic components of the cube were neutralized and the technology left essentially unharmed.
The Cube seen in "Unity" was damaged, but intact, and functional enough that what was apparently a minor repair to a single subsystem resulted in the vessel's reactivation, along with its remaining drone compliment. The Cube was cut off from the collective. I believe it is later implied that the "electrical discharge" which caused the Cube to shut down was actually an 8472 weapon. If Cubes have always been sentient and capable of self-repair and activation without input from the Collective consciousness, why did this Cube not effect necessary repairs itself and bring the deactivated drones back online? Why did it not simply grow a new Interlink Node?
Even if that were true (and I don't agree that it is), that was the whole point of the story: that what we were seeing was something new resulting from extraordinary circumstances. There was never any indication prior to "Elementary, Dear Data" that a holodeck character could become sentient, but it happened there, and happened again later on.
I concede the principle, but not its applicability in this case; by making these new abilities retroactive, the author is not suggesting that this is a unique scenario, and in doing so asks the reader to engage in mental gymnastics to explain why we never saw this occur on screen, or in any prior fiction regarding the Borg.
The Collective consciousness is the Borg, without that, nanites become dormant, drones revert to individuality or die, and without those to maintain it - technology becomes inert. For me personally, it's simply too much of a stretch to assert out of nowhere that, well, actually, cubes are sentient see?
But you're making the entirely unsupported assumption that the collective consciousness consists
solely of the organic minds within it. When have we
ever been given any reason to believe that? We've always been shown that the Borg are a complete symbiosis of the organic and the technological. It's completely misunderstanding them to treat the technology as mere support for the biology, when all along their actions have shown just the opposite, that their organic components (drones) are treated merely as subordinate adjuncts to the governing machinery. Or, at most, that the Borg consider both biological and technological components to be of equal and interchangeable importance.
I do not suggest that the Borg are defined by their organic component, however I do assert that, based on everything we see prior to the events of this book, that the biological minds of the drones are a core part of their guiding consciousness. The whole point of the Borg is not that they are AI, or technologically advanced humanoids, but that through a synthesis of mind and machine have created a new state of being and, alas for everyone else, a rather limited perspective on other forms of life.
The collective itself is a synthesis of all of its component minds; could an artificial mind be a part of that synthesis? Of course, but the specific suggestion that the Borg's space craft are artificial minds, and almost always have been, is what I'm taking issue with.
And they're made up of nanites, see? Oh yes, and they can also puppet drones, and make "pseudo-queens", and suck people into walls, and and and etc etc.
Agree to disagree I suppose.
All of those are extrapolations from things we canonically know to be true. We know their technology includes nanites and is grown by nanites, therefore it's not a fundamentally incompatible premise to posit that their technology could be fully nanotechnological. Even if most Borg technology isn't, this was an outlying cube that
Resistance already portrayed as having some differences from most Borg populations we've seen (such as being sexless by default), so who's to say it couldn't have had some unusual variant of Borg technology as well?
Aha! Hoisted by your own petard(sorry, I've been waiting to use that one for months

); in your own book, you explain the sexless drones as a function of them being "vat grown" rather than assimilated, and that the prevalence of said drones was a function of their distance from the core of Borg territory, in order to guard against them returning to individuality in the event they are severed from the collective. Even if the author
had used a similar reason, which they did not, to explain the actions of the Cube, why would the Borg create a failsafe which specifically causes the rise of an individual consciousness under the same circumstances? Surely they would have followed the same pattern as with other instances of isolation; basic directives to return, or to self-destruct.
As for "puppeting drones," that's what they always do -- the drones are merely peripheral devices controlled by the collective consciousness. I don't know why you'd think that's anything new. If you mean the technology manipulating a dead drone body, zombie-style, we saw something very like that happen in VGR: "Unity." The Doctor inadvertently activated a backup power cell in the dead drone he was autopsying, causing it to rise up and flail around. That proves, canonically, that it is possible for a drone's cybernetic components to cause it to move without there being any living tissue within it.
As for making "pseudo-queens," how is that any more implausible than their ability to assimilate people in the first place? After all, the Queen is simply a specialized drone that contains the Royal Protocol, the software that's essentially the Borg Queen's consciousness. Homecoming/The Farther Shore already established that the Protocol can be downloaded into an assimilated drone. There may be some variations in the way it occurs in Before Dishonor, but there's nothing about the basic premise that's implausible or inconsistent in light of what's been established about the Borg in the past.
I disagree. Drones are not puppets to the Collective in the same sense as they were in this story. Specific drones may be considered disposable if necessary, and they may be controlled by the will of the Collective, but they are also
part of the collective; in this case they were simply macro-nanites, tools being directly manipulated by the singular intelligence which arose from the Cube. I'm not disputing that the mechanism would not allow such a thing, I'm disputing that Cubes have the capacity to do it.
The queen is even more implausible since, again, this is not the Collective instituting the established system to give rise to a new queen, it is the Cube creating for itself a method to control drones, and to gain knowledge from Janeway.
As for the walls being dynamic and mutable, able to change shape or suck people in, I've already pointed out that we have canonical precedent for this going back to "Q Who," when we saw a damaged portion of a Borg cube healing under its own power, morphing back toward an intact condition. So that ability has been implicit in what we've known about the Borg quite literally from the beginning. This was merely an extrapolation from existing canonical precedents.
I disagree, the abilities you discuss are entirely within the abilities of Constructor nanites which are conducting repairs to an existing structure which has been damaged. In addition, in every other case that we've seen,
serious and extensive damage has always required the aid of drones to repair, yet the Cube in BD simply consumes its own mass and does its best impression of a T1000. The ability to
repair damage is not in question, the ability to absorb people, or even entire starships, into the physical structure of the vessel, in seconds, is what I'm questioning, and such an ability is not a reasonable evolution of the Borg's abilities, not in a single stage.
No matter how much pressure natural selection places on a fish, it cannot become a mammal in one step. If the writer had tones down the abilities and implied they were new, or they had developed gradually over a multiple-tome storyline, or even if they had been foreshadowed in other books by insinuating the Borg had assimilated such technology, then the circumstances described in the book would not be nearly as implausible; but to go from the Borg as seen in Voyager to the Borg seen in BD without any significant intermediary steps is exactly that.
In contrast, I can read your book, read the "evolved" abilities of the Einstein/Frankenstein Borg, and see a logical and plausible progression from the Borg seen before.
I maintain that you
must have that connection, that progression, no matter how extraordinary the circumstances of your story, because otherwise it hobbles my willing suspension of disbelief.