Bounty is M50 for a good recommendation, M100+ if I really like it.
"Medium-to-long" means anything normal-novel-length or higher, and longer is better.
Things I like (and will thus make me more likely to enjoy the recommendation):
Time loops
Trans stories (either very clearly thematically trans, or with trans focal characters)
Gay
Science fiction
Fantasy that's written like science fiction
Rationalist fiction
Oh, I like furries- I read actually very little furry stuff, so that might actually be a very likely place to find something easily
I like basically everything on https://recordcrash.com/list/main, so none of the recs on that site count, but it's a good list to get a stronger idea of what I like.
I am very likely to give M100 or more for a recommendation with the first 3 things on that list, and one or more of the next 3. I do, however, enjoy things with few-to-none of the things on that list, it's just less likely.
Webfiction or traditional fiction are both fine, as are fanfics but I'm less likely to pick them (if it's not a fandom I already read fanfic for, I will have a harder time "getting into" the story). Comics, movies, etc. do not apply.
I'm gonna also restrict this to relatively non-horny works. For the moment, I'm good in that respect. A little bit is fine- I actually hate it when stories avoid sex too heavily, but I don't need anything as-or-more intentionally-horny than, say, planecrash.
Related questions
I've got taste somewhat overlapping yours, I think, judging by that list you linked. So, with that said, here's a scattershot bundle of recommendations for the medium-to-long subset of prose fiction-in-this-broad-space which I've enjoyed. (Mostly fanfic, since that's a lot of what I read, especially after filtering for non-horniness and for nonpresence on the Shills List; but probably you'll be familiar with some of the canons, and some of the stories stand pretty well even absent canon-familiarity, so I figure it's worth a shot nonetheless.)
The Rainflower Game: Original mystery story, doing some interestingly unconventional things with the murdergame subgenre. Trans, gay, sci-fi, 270k words, probably dead.
The Moon's Apprentice: My Little Pony fanfic, alternate universe in which Nightmare Moon is somewhat saner than in canon and takes on Twilight Sparkle as a student. Gay, fantasy-written-like-sci-fi, rationalist, arguably furry, 410k words, complete.
The World As It Appears To Be: Overwatch fanfic. Various members of Overwatch do their best to understand the world they're in, why it works the way it does, and how to make it better. Rationalist, sci-fi, 130k words, complete.
To The Stars: Madoka Magica fanfic, far-future sci-fi set a few hundred years after the show, magical girls try to help stop an alien invasion and unravel the conspiracies surrounding it. Gay, sci-fi and fantasy-written-like-sci-fi coexisting, 900k words, in progress.
Of The Stars: Sailor Moon fanfic/~retelling, comprehensible without canon-knowledge, with a focus on adding rigor and detail to the worldbuilding. Gay, fantasy-written-like-sci-fi, 120k words, probably dead.
Wanderlust of the Golden Witch: Umineko fanfic, with Big Spoilers for canon right from the beginning. Alternate universe where Battler doesn't exist and Rudolf's eldest kid is a trans girl. Many divergences result from this. Trans, gay, 200k words, complete.
Silent Partner, Unfinished Business: Death Note fanfic (technically a crossover but the crossover-half is comprehensible without canon-knowledge), alternate universe where Naomi teams up with Misa to try to find Kira. Is the only Death Note fanfic I've read to feature ~canon-tier Elaborate Plotting. Gay, arguably rationalist, 180k words, complete.
Riley, Alone: Worm fanfic, canon-divergence where the Slaughterhouse Nine fall apart earlier than in canon and Riley is forced to learn to build a life in their absence. Trans, arguably furry, 90k words, complete.
Game Theory (and its sequel Power Games): Magical Girl Lyrical Nanoha fanfic, canon-divergence where Precia is saner than in canon and divergences slowly accumulate downstream of that (until eventually it stops being so slow). By the same authors as Of The Stars, with a similar focus on worldbuilding rigor/detail. Fantasy-written-like-sci-fi, 250k words per story, both stories complete.
Fairy Dance of Death: Sword Art Online alternate-universe fanfic, comprehensible without canon-knowledge. Twenty thousand people get trapped in a PvP deathgame; international politics ensue as the different factions do their best to keep civilization functional enough to let them work together on their shared goal of Not Dying, with the story being told from a variety of viewpoint characters involved in different pivotal events throughout the world. Sci-fi, 740k words, in progress.
Dungeon Keeper Ami: Sailor Moon/Dungeon Keeper crossover-fanfic, comprehensible without canon-knowledge. Magical girl gets stuck as a dungeon keeper in a world where dungeon keepers are almost always very evil; isn't very evil; does her best to survive the attacks of all the people who oppose her as a result of this state of affairs through the power of Clever Engineering. Fantasy-written-like-sci-fi, 890k words, probably dead.
Too Like the Lightning checks all of those boxes except furries
I hesitate to suggest this in the Year of Our Lord 2023, but… Homestuck?
The only traditional book that comes to mind is a short-ish YA novel called “Every Day” by David Levithan. Well written, but might be a bit vanilla for you based on your criteria.
Otherwise you should take a look at Steins;Gate (the anime or visual novel)
I share some of your tastes so I’m really frustrated I can’t think of a great time loop novel off the top of my head lol. I love that stuff. The most “cerebral” time loop-ish novel that I’ve ever read and enjoyed was Eleanor Catton’s “The Luminaries,” but be warned that the book is capital-l Literature and makes no apologies about being such.
Supposedly “Recursion” by Blake Crouch is coming to Netflix soon? Never read it personally tho.
Other than that, you could always read the source material for Edge of Tomorrow (All You Need Is Kill).
But something that satisfies all of your bullet points is almost certainly a hentai game, but your description rules that out…. Hmmm. So many books, and yet so few that satisfy those criteria…
Mother of Learning by Nobody103 - "an amazing progression fantasy webnovel that has time loops, loads of different magic, and great characters." https://www.royalroad.com/fiction/21220/mother-of-learning
Ra - "Magic is real. Discovered in the 1970s, magic is now a bona fide field of engineering. There's magic in heavy industry and magic in your home. It's what's next after electricity." https://qntm.org/ra
Fine Structure -"Fledgling physicist Ching-Yu Kuang has discovered a Rosetta Stone for all of physics, a treasure trove of advanced scientific breakthroughs beyond all imagination. Exotic energy, teleportation, FTL, parallel universes and near-infinitely more wonders are just within reach; a promise of paradise.
But every attempt to exploit this new science results in sabotage, chaos and destruction. And the laws of science themselves are changing with each experiment, locking out the new discoveries, directly altering the universe to make what should be possible impossible. While Ching watches, humanity's future is being stolen." https://qntm.org/structure
The Wandering Inn by Pirateaba. Because you said longer the better, and it comes in a whopping 7.5 million words!
"The Wandering Inn by Pirateaba is one of the most beloved web serials with the most loyal fans. It is an incredible series.
The Wandering Inn is a comfy, slice-of-life web serial with litRPG elements. Imagine playing a videogame where you are an innkeeper in a fantasy world. You would meet characters from all different backgrounds and probably go on a sidequest or two with them. Now, put that concept into a literary format, and you’ve got this web serial.
The Wandering Inn is an extremely captivating story from start to finish. It might take you a while to get there, considering there are 7 volumes, and it is still ongoing. If that seems intimidating, don’t worry. Maybe the audiobook will make things easier.
I can’t recommend the audiobook enough. Andrea Parsneau truly manages to bring the world and its huge cast of characters to life."
https://wanderinginn.com/ (or https://www.audible.com/pd/The-Wandering-Inn-Audiobook/1774240327 )