First off, I really love HPMoR. I really do. I love the science. I love the humor. I love watching the main character turning so deliciously evil. The vast majority of HPMoR is well-written, clever, and appeals to me in particular because I just fall all over this stuff anyway. And obviously, a lot of people agree with me.
But like all books, it has its flaws: pretentiousness, euro-centricity, sexism and an overwhelmingly ooc Harry Sue, to name some of the most annoying. But unlike some books, the flaws in HPMoR aren't just parts of the story that fall flat. They are actively in your face annoying. They're distracting while you're trying to enjoy the good parts. As i suggested in my title, its like trying to enjoy a snickers bar that's embedded with very tiny pieces of gravel. I find myself struggling to enjoy the story and ignore the flaws, even though i usually have no trouble at all only remembering the good.
Overall, HPMoR is unique, wonderfully written, and exceedingly annoying to read. I love this fanfic, but I hate reading it.
Of course, that only applies if you like the good stuff in the first place. If the stuff I love falls flat for you (I know some people don't enjoy reading about evil people, for example) then no way in hell will you enjoy it at all. In fact, I fully understand the people who hate this story.
For instance. I cant stand the Hermione in this fic. She refuses to listen to reason, shes unambigously good, and she whines a lot. Plus, she argues in favor of objective morality, which is awful. spoliers
(note cause my spoilers tag isnt working for some reason)
I also despise James, and think Lily should have been with Snape. HPMoR supports my feelings on the matter. Neville is awesome. The main character is turning evil, possibly my favorite part of the story, but I know some people prefer their heroes to be, well, heroic.
In general, I may be biased because the fic appeals to me personally. But I still feel that if you enjoy morally ambigious heroes, logic, and really really funny characters, and you can stand sexism and egocentric writers, this is the fic for you.
Prepare to be amused and irritated.