It's a great deal of fun, but it was written by an Awesomeness Maximiser (or at least an initiate of the Awesome Conspiracy), not a rationalist. What the fic shares with MoR is not a lack of the Idiot Ball, but a sense of... embiggening, as if walls around the canon were suddenly removed. I don't know how better to put it.
Actually, a good comparison of 40K!Shinji and MoR!Harry would be illuminating, but I'd have to reread it before trying. There are parallels, although the former's mental uberness is more along Paul Atreides lines - the details aren't quite there.
I imagine it also depends on how much you know/like the two settings, because that conjunction magnifies the effect (for me at least). 40K is a setting composed entirely of insane heroism in the face of death. NGE is a setting where the whole world desperately yearns for awesome, but the flawed hero's inability to deliver awesome brings everything crashing down. To some extent, every NGE fanfic is a Fix Fic, because the canon just hurts so much.
Using 40K as the patch happens to work really, really well. Canon!Shinji would be incapable of casting the True Patronus. 40K!Shinji pretty much IS one.
Update: Discussion has moved on to a new thread.
After 61 chapters of Harry Potter and the Methods of Rationality and 5 discussion threads with over 500 comments each, HPMOR discussion has graduated from the main page and moved into the Less Wrong discussion section (which seems like a more appropriate location). You can post all of your insights, speculation, and, well, discussion about Eliezer Yudkowsky's Harry Potter fanfic here.
Previous threads are available under the harry_potter tag on the main page (or: one, two, three, four, five); this and future threads will be found under the discussion section tag (since there is a separate tag system for the discussion section). See also the author page for (almost) all things HPMOR, and AdeleneDawner's Author's Notes archive for one thing that the author page is missing.
As a reminder, it's useful to indicate at the start of your comment which chapter you are commenting on. Time passes but your comment stays the same.
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: