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So this is a thing that I've started to contemplate while discussing fanfic peeves and whatnot with tanithryudo. I am of the belief that fanfic's job is not to slavishly follow canon, but rather to transform canon into something new. But why is it that when certain elements get altered it feels completely fine while other elements feel like it violated fanfic expectations?
I'm not sure I have a real answer, but I think it might come down to what the reader perceives as flavor vs framework in a story.
Flavor is, vaguely, elements to the canon world building that don't fundamentally alter the plot. Framework, on the other hand, are elements that are so woven into the story's plot advancement/character development that altering it would require extensive re-writing for the story to keep its internal logic consistent.
I will try to demonstrate this via a fantasy comparison and a sci-fi comparison. Note this is not some kind of absolute categorization nor is it a universally agreed upon mechanism. This is merely my shallow attempt at explaining why certain fanfic succeed at transforming the canon while others fail from my perspective.
Magic as flavor in fantasy
In my opinion, magic in the world of Harry Potter is flavor. The core story is focused on a special kid who goes to school and has lots of adventures. The adventures get dangerous as the story progresses and culminates into a giant fight with the bad guy.
In this story, magic is merely a set dressing, the flavor if you will. The social dynamics are dictated not by the magic of the world but rather by the fact that the story of Harry Potter is set in a (magical) boarding school that's far from modern civilization and the school itself feeds the interpersonal conflict via a House system. The Houses in Hogwarts are divided by personality and there's an implication that certain personalities are more prone to becoming evil.
Replace the magic of the Harry Potter world and the same conflicts remain. Draco will still be a mean kid. The Weasleys will still be a poor family. Hermione will still be an outsider who was brought into the cloistered society. The concept of "pureblood" will still apply to the characters all the same because the concept is based on bloodline, not magical pureness or some other magic-adjacent measure. As such, the exact same story could be told with minimal changes when swapping magic out for technological equivalents. There is nothing about the story of Harry Potter that dictates it has to contain magic other than the fact that magic is flavorful.
Ergo, a Harry Potter fanfic that is set in modern English boarding school or even a Victorian era boarding school wouldn't feel out of place. But set Harry Potter in a magical equivalent of, say, modern USA, and suddenly the story as it is told doesn't work nearly as well. This is because while the flavoring is kept, the fundamental framework (in this case, the accepted striation of society based on class and importance of bloodline/aristocracy) do not hold the same amount of cultural valence in a democratic and federalist system that's fundamental to the USA. Put Harry Potter in a magical US high school and suddenly the personal relationship dynamics and the causes of social conflict have to change in order for the story to stay internally coherent.
Magic as framework in fantasy
In contrast, in a work like Lord of the Rings, magic is part of the story's framework. Magic is the reason Frodo is drained of the will to live by the end of Lord of the Rings. Of course there is the experience of the journey itself, but without the magical One Ring and its evil magic literally sucking the life force out of Frodo, Frodo would not become a shell of himself. The trials of the journey are not nearly bad enough to make Frodo become unable to feel happiness whatsoever.
Similarly, the conflicts between the characters are heavily driven by the existence of magic. While there are some social causes and personal causes (like greed, hubris, jealousy, etc.), those problems are preyed upon and exacerbated by the evil magic. The story is written such that without magic as the final push, the bad characters would not have fallen. Golem's obsession, Borimir's bad decision making, Théoden's acceptance of Wyrmtongue, Denethor's usurpation of power, Sauruman's everything... All the major conflicts could never have happened without magic. If magic did not exist in Lord of the Rings, the story simply cannot progress as it did.
But, change the medieval setting to, say, magical Edo Japan, and the general premise of the story will still remain intact. Yeah, you'll have the change the names and take into consideration how daimyo aren't an exact replacement for kings of feudal England, but the basic plot points can still carry on just fine.
Take the magic away, however, and replace it with just greed or hubris or replace the One Ring with a technological MacGuffin and none of the motivations makes any sense anymore. Magic is part of the story's framework and thus non-negotiable to the story of Lord of the Rings. A Lord of the Rings fanfic that doesn't keep the magic will need to develop a lot of original explanations into the story to justify the character motivations and conflicts.
Science as flavor in sci-fi
I would argue that in Star Wars, the science is very much unnecessary. Given how poorly the "science" of The Force was accepted (does anyone like the midi-chlorian explanation?), I would go as far as to say the science is being actively repelled by the story of Star Wars.
The focus of Star Wars is the political struggle of resistance against a government. The exact nature of the struggle is actually unimportant (and poorly explained). Other than knowing government evil, resistance good, laser swords go bzz and troopers pew pew, there's not much else you really need to know about the world to understand the main conflict of the story. The good guys don't want to kill a bazillion people. The bad guys do.
Put the story of Star Wars into basically any setting where the government is doing a bad and the resistance is resisting said bad, find an excuse for some sword fights to happen, and you've got effectively the Star Wars story. Now, it's fair to say that without the flavor of Star Wars (The Force, Jedi, lightsabers, stroomtroopers, etc.) and you won't have Star Wars, you'd just have "another resistance fights the government story". But that's also kind of my point.
Star Wars is just another resistance fights the government story. And for a lot of people the flavor is actually the main draw, not the framework of the story. But simultaneously, the reason Star Wars is popular is because the framework "resistance fights the government" is popular. And we know this because The Hidden Fortress, a Kurosawa film that inspired Star Wars, is also very popular. And it's no coincidence that these two film fandoms have a large overlap (especially among the American audiences), especially in light of Star Wars being ostensibly sci-fi and The Hidden Fortress is a period drama.
So while I don't deny that flavor is very important for whether someone likes a work, the framework of said work is also very important. And for some audiences, the draw of the framework is more important than the flavor.
Science as framework in sci-fi
In Star Trek, the science, no matter how speculative and unsound, is absolutely essential to the story of Star Trek. Not only is the fundamental ethos of the Federation's exploratory star fleet tied up with the discovery/exploration ethos of science, but much of the social dynamics are designed through a scientific lens. That is, social sciences and evolution play a major part of how "alien" societies are conceptualized within the narrative. Yes, there are flaws, but having a scientific explanation is important to Star Trek's story. Because it is from that scientific cause of the conflict that a solution is derived when it comes time to solve the conflict being addressed in each episode.
Tribbles need food to breed, Q's powers are the result of extra-dimensional physics, warp drives need to compact space-time continuum with an engine...ergo Tribbles must be removed before eating the entire food supply, Q cannot be understood with 3rd dimensional physics, space ships can't warp if the engine breaks. Everything has a direct cause and effect that cannot escape the material constraints of the world. Again, this might not be perfectly executed every time and writers forget the rules they set up earlier in the series, but the story nonetheless focuses on telling the causation-reaction chain of events as the main advancement of the plot.
Remove science (and the scientific approach) from the story and the story would have very, very little left to drive the plot forward. Do we actually care about Kirk's romantic conquests? Does Riker's lady-killer reputation actually matter? Is anyone actually interested in debating the Prime Directive's ethical reasoning? No. At least the story isn't interested in it. (And if you are interested...well, again this is where fanfic steps in...)
Now, as a reader of slash fic/BL fic, I've become quite comfortable with accepting a wide, wide amount of deviation from canon. I will defend deviation and transformation of canon to the end, but I do think it's important to identify what parts of canon is being changed and whether that change affects flavor or framework. Correctly identifying the nature of the change and addressing the effect of that change is what makes transformative works fun. Failing to correctly identify the nature of the change and simply slapping a plot into a setting results in fics that, at least for me, no longer feel like fanfic.
At that point, one really is better off just writing original fic.