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Notes -
I didn't like Mother of Learning. It's literally just Time Braid*, but worse†.
If you want the best the web novel medium has to offer, I'd recommend Worth the Candle by Alexander Wales‡.
* Zorian is Sakura, Zach is Naruto, Red Robe is Sasuke, QI is Orochiramu, they are all trapped in a one-month time loop that ends with an invasion, etc.; it's obvious once you know Domagoj Kurmaic listed Time Braid as one of his favorite stories on FanFiction.Net.
† Mother of Learning is slower, the fights are less exciting, the characters are flatter, and there is less fanservice.
‡ Unless glowfic counts, in which case I'd recommend Project Lawful by Eliezer Yudkowsky (LessWrong) and Kelsey Piper (The Unit of Caring).
I want the best medium-length web novel medium has to offer. Wales is good, but if I remember correctly, he's not known for brevity.
Wales actually has a handful of great short stories. IMHO they're better on average than his long fiction!
Also, although I loved Worth the Candle, it's long and some of its twists and turns are controversial. IMHO every revelation was utterly sensible in hindsight and made a good story even better, but de gustibus non disputandum, and I recognize that if I didn't like a major twist after I'd read 200-odd chapters to get to it I'd be massively disappointed.
You might try his The Metropolitan Man. Fan fiction, but a great combination of clever reconstructions and deconstructions that lead to unique differences from the canon. 80k words, so more "short-length web novel" than medium-length, though.
Seeing the Wales discussion, I was going to mention Metropolitan Man. Quite possibly my favorite Rationalist story, not least because it's one of a handful of well-made art pieces that I love for very clearly elucidating a perspective I strongly disagree with. It's simultaneously the best argument for and against Rationalism that I've seen.
I'd love to find out what you're talking about here. The obvious candidate that jumps to mind isLex Luthor's rational but ultimately self-destructive analysis of Superman-as-existential-threat but although that's one of the most fascinating parts of the book, it's a classic villain elucidating a perspective that even the author, albeit non-clearly, disagrees with and once I start thinking of less-obvious candidates ... well, I don't mean "what are you talking about?" in the idiomatic "you sound crazy" sense, but in the literal "there are like five things you could be talking about but I'm not sure which it is" sense.
Is there author commentary somewhere? My read was thatLuthor did the rationally-correct thing, that the benefits of Superman weren't worth the existential risk, and the ambiguity just drives home the idea that Rationalism is a gamble, and the best you can do is make smart bets. In what sense would Wales disagree with that position?
What were the other five things? I really ought to read it again.
I haven't read author commentary, so you could be right. My read is thatLuthor might have been doing the rationally-correct thing in a world where only Superman exists, but in a world where Superman is just a single example of a whole class of existential threats (which is likely from Luthor's perspective, a priori, and which would be certain if this universe actually matched the DC universe, and which arguably includes Luthor himself futzing around with Kryptonian technology), the risk of Superman turning on us if left alive is less than the extra risk of meeting others among those threats without Superman to help.
IIRC the other big perspectives that might engender disagreement (or stronger disagreement, when there's disagreement presented in-story):
The thing I remember most about Lois in the fic is that her thottery pisses off Superman, which is sadly in-character.
Now I know where Something Unlimited got its art style from!
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