The character should somehow reflect on the stupidity of others; whether by frustration from their inability to cooperate, or by enjoyment of how easily they are manipulated.

I'm not sure I like that criteria. By that criteria alone, the original death note anime was rationalist fiction (judging by the first half), as is Artemis Fowl, Ender's Game, and to some extent even Game of Thrones. There are a lot of stories where some characters are much smarter than others and know it, but consuming these works won't teach anyone how to be smarter. (Other than the extent to which reading good fiction in general improves various things)

None of these stories actually teach the reader anything about epistemology. Even the linked Death Note fan fic...it uses rationality-associated words like "utility" and "prior" but if I didn't already know what those words meant I would have just come away confused. (Granted, it's still early in the story - but even so)

Also, it hasn't yet broken the conceit of the story (For example, even a normal person of average intelligence would be surprised and curious about the existence of the supernatural, and would investigate that). I'd say that breaking the story conceit is another feature of rationalist fanfiction stories that has nothing to do with the character's intelligence.