You said:
...which I read as saying that writers should only look at the "quality" lore and ignore the rest.
No, not ignore the rest... update, change, correct and improve it, using the "quality" lore (such as written by the authors I mentioned) as a source of inspiration. As an example, I wish they had "corrected" Halaster's appearance (which was unfortunately "reimagined" in 'Escape from Undermountain') to match Ed's more sinister vision in the Undermountain Boxed Set. Of course, if the information is already updated in another source, and there's no logical reason to "mess" with that, you could ignore the original source.
With over 20 years of published material (including novel lines and Dragon articles), I don't think it's so simple. Also, information about topics tends to get spread around; it's not enough to simply look at the stuff that is supposed to be focusing on the subject. I see this a lot in Eberron, where information on the structure of the Church of the Silver Flame can be found in the ECS, the Eberron Player's Guide, Sharn: City of Towers, Five Nations, and Faiths of Eberron (some of it contradictory). And there's probably other details added in other books that I don't own, as well... It's not as simple as saying, "Oh, Silver Flame, I'll grab the ECS and Faiths of Eberron and I'm good."
Which was kind of my point, i.e. that it's not much easier to research Eberron lore than FR lore. Now, as I admit below, I was wrong about the number of Eberron supplements, which makes it easier than I claimed, but in time I'll have no doubt that Eberron will be just as much "burdened" by lore as FR was perceived to be. I hope to be wrong, but I have a hunch that in a couple of years FR will become a setting for novels without any DDi support anymore.
Information seeking is not that hard; bibliographies and indexes (such as the Dragondex for all the FR articles) help there a lot. Of course, in some cases small details (such as about religions) may be included in books that do not seem relevant, but then again, it may not always be absolutely necessary to read all the "tidbits". For example, if I'm not dealing with the "deepest" layer of details with the Church of the Silver Flame, the newest sources may be enough for my project.
And, as I have already said, newest FR material "trumps" older lore (such as, sadly, with Halaster's appearance); I suspect that this also the case with Eberron, too, so if ECS and Faiths of Eberron have contradictory details, you go with what's in FoE.
No argument there. I think they could have achieved much of the same results, with less outcry, simply by advancing the timeline far enough and retconning the edition differences (in much the same way as sorcerers were retconned in and specialty priests retconned out with 3e).
Many specialty priests actually were later published as prestige classes, such as they're now being published as paragon paths -- both working solutions, in my opinion.
I don't think advancing the timeline or the Spellplague were obligatory for implementing 4E changes; it could have been done in other ways. If Mystra and her Chosen really, *really* absolutely had to be taken out of the picture, this, too, could have been in ways that make sense. For example, Shar's "decline" hinted at in 3E lore and the events of the last adventure trilogy could have resulted in "corruption" of the Weave and Mystra's descent into madness. As her final, desperate act, she and the other deities of Magic would have sacrificed themselves, to "fix"/rebuild the Weave in a new form (i.e. to confirm to the 4E mechanics); the backlash of the deaths of these deities would have driven the Chosen mad, and diminished Shar's power as the Shadow Weave would have been affected, too. AO, not Shar, would have then decreed that no new deity shall hold power over the "New Weave", thus leaving the pantheon without a deity of magic. I don't know about you, but that would make more sense to me than the current "story", and yet accomplished the same (sans destroying the Weave, naturally).
Unless I've simply missed a ton of WotC's marketing, that number looks to be at least two times too large.
Actually, it seems that you're correct; my bad. I didn't check the number of Eberron titles before posting, which was unprofessional of me. I guess I just trusted on my memory, i.e. reading/hearing about "50+ Eberron books", but didn't realize it included novels as well. Sorry about that.