A few months ago, I re-read HPMOR in its entirety, and had an insight about the Hermione / feminism issue that I'd previously missed when I wrote this comment. I never got around to saying it anywhere, so I'm saying it here:

I'd previously written:

HPMOR kinda feels off because canonically, Hermione is unambiguously the most competent person in Harry's year, and has a good chance of growing up to be the most competent person in the 'verse. Harry is kept at the center of the story by his magical connection to Voldemort. In HPMOR, in contrast, Harry is kept at the center of the story by competence and drive. It's going to be very hard to do that without it feeling like Hermione is getting shafted.

But actually, HPMOR closely parallels cannon on this point: Methods!Hermione got just as much of an intelligence upgrade as Methods!Harry did, so she's still unambiguously more competent than him, at least before repeated use of his mysterious dark side gave him a mental age-up. This is more or less explicitly pointed out in chapter 21:

She'd done better than him in every single class they'd taken. (Except for broomstick riding which was like gym class, it didn't count.) She'd gotten real House points almost every day of their first week, not for weird heroic things, but smart things like learning spells quickly and helping other students. She knew those kinds of House points were better, and the best part was, Harry Potter knew it too. She could see it in his eyes every time she won another real House point.

The that the universe is being grossly unfair to Hermione, and this is hammered home multiple times. E.g. I can't find it at the moment but I think there's a scene where Harry explains to her she can't get house points for telling adults about the secret message in the Sorting Hat. Or there's this exchange in the Self-Actualization arc (emphasis added):

She couldn't find words. She'd never been able to find words. "If you get too near Harry - you get swallowed up, and no one sees you any more, you're just something of his, everyone thinks the whole world revolves around him and..." She didn't have the words.

The old wizard nodded slowly. "It is indeed an unjust world we live in, Miss Granger. All the world now knows that it is I who defeated Grindelwald, and fewer remember Elizabeth Beckett who died opening the way so I could pass through. And yet she is remembered. Harry Potter is the hero of this play, Miss Granger; the world does revolve around him. He is destined for great things; and I ween that in time the name of Albus Dumbledore will be remembered as Harry Potter's mysterious old wizard, more than for anything else I have done. And perhaps the name of Hermione Granger will be remembered as his companion, if you prove worthy of it in your day. For this I tell you true: never will you find more glory on your own, than in Harry Potter's company."

I think what happened is that Eliezer realized how unfair the universe was to Hermione in canon, and decided to keep things that way in HPMOR but comment on it. Which is clever, but looks like Eliezer being unfair to Hermione for no good reason if you don't understand he's commenting on the screwiness of canon.

Related thing I noticed: Hermione is probably the most incredibly brave character in HPMOR. Think about it: she, as a twelve year old girl, is told she has an important job to do helping Harry, and then one of the scariest dark wizards who ever lived tries destroy her, when he doesn't succeed at that, tries to convince her to just run, and she stands her ground. As a twelve year old girl against an ultra-powerful dark wizard. And that's ultimately why she died. Make no mistake about it: she died a hero's death.

Edit: this is relevant.