atorm comments on Harry Potter and the Methods of Rationality discussion thread, part 22, chapter 93 - Less Wrong
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Eliezer has said that Hermione hasn't been powered up as much as other characters because she was already so great in canon. This is one voice who hasn't had any issues with Eliezer's handling of Hermione.
And went so far as to observe that if Hermione were to be upgraded in the same way that Harry, Quirell and Draco had been upgraded then she would surpass the intellectual capabilities of the author himself, and his ability to emulate.
It's possible to write about characters cleverer than oneself by two means I can think of.
having unlimited time to think about what your character arrives at in an instant
getting multiple people to help with the above.
But at some point your character is going to think about something for more than an instant (if they don't then I strongly contest that they are very intelligent). In a best case scenario, it will take you a very long time to write this story, but I think there's some extent to which being more intelligent widens the range of thoughts you can think of ever.
It's going to take a very long time for Chimpanzees to write Hamlet.
Sure, the method I mention only allows you to write characters a single level above yours.
You can also have characters make original discoveries that you read about in books.
Or correctly apply in real time techniques that you have only read about in books.
As Harry himself points out, Harry is cheating, and hard. He has a dark-side, he has a time turner, he's been training his mind from birth... and Hermione is still beating him in raw intelligence, and was just starting to learn to be a hero before her death.
Aside from that, take a look at Hermione Granger and the Burden of Responsibility, which is a recursive fanfiction of HPMoR diverging during her trial. It's really only just getting started, but I have hopes.
I've just read the first chapter and this is excellent. Though I'm concerned that the title indicates that it might culminate in Hermonie angst-mongering. If that happens, I might just start a fanfic of order 3 with Amelia Bones as the main character.
Yes, I'm starting to think of Spider-Man. But I don't expect this story to go that way.
Hermione wasn't powered up at all.