Now that it's finally done, the last chapter posted and read, I feel I can at last whole-heartedly recommend Harry Potter and the Methods of Rationality. I've been reading the damn thing for nearly five years.
The thing I noticed most strongly about the ending is that the author didn't drop a single stitch. Everything about the story makes sense and is complete. Any number of things that were odd or confusing as they happened are explained--explained wonderfully, even--by the time we get to the final chapter. Nearly every complaint I have about the story is either entirely resolved or justified in-story. It's a remarkable feat, and I suspect I'll be comparing my own writing and finding it wanting for years to come.
The premise of this story is that Harry was raised by an Oxford professor and given an absurd love for science and rationality. He's an unholy mixture of Ender, Miles Vorkosigan, and Artemis Fowl. Which sounds ridiculous, right? How can anything pose a challenge to someone like that?
Luckily, the Voldemort of this story is himself a ridiculous mastermind genius.
If this sounds at all appealing, check out the first few chapters. I suggest reading at least up to the chapter where the Sorting Hat [redacted], because that's where the premise really starts making things fun.
Caveats: yeah, it's fanfic. And it's kinda didactic. And HJPEV is a little insufferable. (Also you may wish to avail yourself of the trigger warning page, under "More Info.")
But damned if the whole thing isn't awesome.
That thing is Artemis Fowl taken to such an extreme that only fanfic can manage. (Not entirely crapping on it, as I can see why it'd be fun.)
I am crapping on the fact that the author wants a hugo nomination and to be put in touch with Rowling so he can publish his fanfic. haha