Warning: As per the official spoiler policy, the following discussion may contain unmarked spoilers for up to the current chapter of the Methods of Rationality. Proceed at your own risk.
Assume HPMOR was written by a super-intelligence implementing the CEV of Eliezer Yudkowsky and assorted literary critics. What would it have written differently?
... is what I want to know, but that's hard to answer. So here's an easier question:
In what ways do you think Eliezer's characterisations/world-building/plot-fu are sub-optimal? <optional> How could they be made less sub-optimal? </optional>
(My own ideas are in the comments.)
To put it another way... Assume a group of intrepid fanfic writers in the late 2020s are planning to write a reboot. What parts of Eliezer's story do you think they should tweak?
And just to make sure we're all on the same page: Eliezer isn't going to go back and change anything he's written to bring it in line with anything suggested here. This is purely an "Ah, just consider the possibilities!" thread.
... which means that we can safely suggest drastic rewrites encompassing 30 chapters or something. Or change fundamental facts about the world.
(Exercise due restraint on this one. Getting rid of the Ministry/the Noble Houses/blood purism would probably turn the story into something completely different; this isn't what we're trying to do here.)
With that, let the nit-picking begin!!
Hmm, how many half-bloods are there? Do we ever really meet a typical half-blood? (Harry isn't really half-blood, and Harry, Snape and Voldemort all had unusual childhoods...)
Muggle-marriers may be a tiny minority. Their existence does not imply that wizards in general get along with muggles, even if there's nothing squicky going on.
From Wikipedia:
Though yes, 'half-blood' here refers to any wizard that isn't muggleborn or pure-blood. So a great deal of them might just be descendents of muggleborns.