I remember some of this stuff differently. To wit:
I can think of a few, though they were all relatively minor. To my mind, Erik is at his best when he's working on a setting he personally enjoys (for that matter, who isn't?) such as Greyhawk or Golarion. When it comes to other settings though...not so much.
For example, back when he was in charge of Polyhedron, he published the ill-received Spelljammer (mini-)setting "Shadow of the Spider Moon" (Polyhedron #151/Dungeon #92). In fact, the troubles with that began in the preceding issue, where his editorial dissed the "silly" nature of the original Spelljammer setting (I believe he called the giff "goofy hippo-men").
I agree that this was a mistake, in that it turned off the folks who were most likely to be interested in a new take on Spelljammer. I chalk this one up to "lessons learned," though I still stand by Shadow of the Spider Moon and in many ways I think it's conceptually stronger than the original Spelljammer campaign setting. But I shouldn't have dissed the Giff.
Then there was an editorial in Dragon where he talked about how the arrangement of the planes didn't make sense (I can't find the specific issue number, apologies). It wasn't anything such as the alignment-based structure of the Great Wheel - rather, he talked about how the planes were largely wasted space (e.g. "can you fly into the sky in an Outer Plane for an infinite distance?"), how being able to go to Heaven made adventuring superfluous (a variant of the old "why not just stay at home instead of adventuring?" argument), and other pokes at the setting.
I suspect the editorial you're referring to was "Please Pass the Ketchup," on page 6 of Dragon #321. That editorial included such observations as: "The planar cosmology of D&D stands out as the most unique and imaginative element of D&D fantasy, a trophy tarnished merely by the fact that the cosmology is also the worst element of the game" and "Sure, we should keep the sacred cows, but the rest should find their way to the chopping block."
Outrageous, you might think! Detestable!
And I'd probably agree with you. Because I didn't write that editorial. That came from the pen of Mr. Matthew Sernett, my immediate predecessor on Dragon, and I remember that editorial driving me up the wall when I first read it. Mostly because I have a soft spot (perhaps much too soft) for stuff that's been part of the game since 1st edition, and the editorial read, to me, like heresy. Reading it now, 7 years later, I don't find it nearly so offensive, but if you want to know the reasoning for all of the changes they made to the Great Wheel in 4e, this editorial is, in retrospect, a nice preview. I still don't like it very much.
I posted a response here on EN World, and to be fair I remember receiving a very nice reply from Erik himself. My basic point was that none of the issues he raised were specific to the planes themselves - the universe around a given campaign world is also wasted space, but nobody worried about that too much (except for those silly fans of SJ

).
Did I? I'd love to see that post, because I'm having a hard time imagining that I might have defended that editorial back then, but I suppose anything is possible. Matt's a great guy, so I may have tried to stick up for him out of solidarity or something. I don't remember this exchange, in any event.
But the big one was the debacle with Dark Sun in Dragon #319 and Polyhedron #169/Dungeon #110. Now, I certainly didn't agree with a lot of the complaints people had (mostly those regarding the setting and timeline), but many of the mechanical issues were rightly disliked - paladins just don't belong on Athas, and sorcerers are a very ill-fit. It got to the point where Dave Noonan publicly outlined how his manuscript had been different, and that the changes in the final product were due to editing.
From what I remember, Erik was rather bitter about that one, saying something to the effect of "some fans just can't be pleased." Again, he's not entirely wrong - some fans of that setting really seem to hate everything after the first boxed set - but his editor's pen clearly took him in the wrong direction where Dark Sun was concerned.
You mean the Dragon #319 that was not edited by me, but by the aforementioned Matthew Sernett? I am guilty of editing the adventure in Dungeon #110 and the associated world and monster info in that issue's Polyhedron section, but I most certainly had nothing to do with the Dragon article that force-fed the paladin and sorcerer into Dark Sun. Poor Matt, I don't even think it was his decision, but rather something Wizards insisted that we did to make it "compatible" with 3e. I certainly don't think I would have posted to the effect of "some fans just can't be pleased," though. I think you're thinking of someone else in this case (again).
For the record, I took over Dragon starting with issue #327 and continued through to the very last issue of Dragon, #359. For many years prior to #327 I edited the Living Greyhawk Journal section of Dragon, but had no editorial control over the rest of the magazine.
Now, to be fair, all of these are minor problems over the course of what's been a truly distinguished career with D&D/Pathfinder. Erik is one of the modern-day giants in the industry, and deservedly so. But nobody does everything perfect all the time, especially where the varied nature of campaign settings are concerned. It's an object lesson, I think, that settings are best written and published by the people who love them the most; anything less than that has a very hard time living up to the fans' expectations.
I'll cop to an inartful insult against D&D's hippo men, but as for the other criticisms, like Grizzly Adams, I'm afraid I've been convicted for crimes I did not commit.
--Erik