I think the topic title is wrong.
When disqus was initiated, the quality of discussion instantly plummeted for the following reasons:
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People no longer had to care enough to create a BB account - which was often difficult and error-prone in the prior systems, it took me five tries because I was using a heavily secured browser. Instead, you just used your existing Google account or whatever. This removed a (rather fickle) barrier to entry so BB started getting less insular and more subject to drive-bys.
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Because it allowed multiple authentication and identification sources, disqus let people engage in massive sock-puppetry. I have around ten valid disqus IDs, personally, although like most people I don’t misuse them (with one exception, to prove a point about disqus). Antinous used to seek out and destroy sock-puppets under the older forum systems, Disqus ended that.
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Because the new system was so radically different, it was more difficult for the moderators to do their jobs. Disemvowelling (which I loved, and which really contributed to the formation of this community) was done manually under the old system (I offered to automate it, but Dean has no reason to trust my coding skillz) and proved to be far too much for the mods to continue in addition to dealing with the normal site traffic and the new requirements of disqus.
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Because of points 1 & 2, people could use their multiple accounts to flag posts that they disagreed with and get them removed without moderator intervention. This created secret moderators who acted to suppress ideas outside the groupthink of the community (something disemvowelling didn’t do, since you could puzzle out the objectionable material if you wanted to, while removing it from casual view).
The faults of discourse fall principally in the same buckets as those of disqus. I do not think that the discussion quality has suffered in any way with the introduction of discourse, although I do fear the departure of Antinous will have negative effects. He certainly kept me in line… and was remarkably fair about it, despite our sometimes vehement differences of opinion.