I spent twenty minutes reading it in reverse chronological order before I thought to check the header bar for chapter reviews. That was a mistake. Dude spends way too much time responding to anonymous hate; it's not fun to read and it can't be fun to write.

Now that I have found the chapter reviews, it's flowing a lot better (though still not perfectly by a long shot). I can sympathize with a lot of the things su3su2u1 found frustrating; I think there's a deep tension between HPMOR as a didactic tract and as a commentary on the canon Potterverse and as porn for nerds, among other things Eliezer's trying to do, and I think the cracks show the most in the early chapters. Similarly for the character of HJPEV himself. Not qualified to comment on the physics, but I did occasionally feel like I was being bullshitted when I was reading the fic.

As to the downvotes, I imagine someone -- two someones, judging by karma -- thinks you're concern trolling. Don't let it bother you.