The bigger problem to me seems to be that great comments that come in a few hours after the posting of a hot submission will almost never reach the top of the comment stack, because older comments that are decent enough will inevitably keep getting upvotes by every new reader of the thread. I'm not sure what the best tweak for that is, but the proposed feature at hand would seem to exacerbate the situation.
Note: OK, I've realized I made the archetypical dickish HN comment ("OK the OP is interesting but on a tangent, why don't we all discuss this other thing I care about?")...but I do think the proposed feature will have a direct impact on the circulation of fresh, insightful comments. I'm a 1000+ Karma user, but after I've read a thread a couple of times, I probably won't re-check it...I can't be the only HN'er who has this lack of attention span...and so this queue, even if perfectly implemented, would seem even more to suppress new comments (unintentionally)
With this new system, I can't imagine YC companies being called out on their dirty closets like they have in the past (any maybe indirectly large swaths of people who are employed by big co's who are power users on HN with those stories, or in general up and coming companies people engage with in the community).
I know some may feel I'm over exaggerating (because there are the passive bans through blocking upvoting/downvoting effects for comments/posts/polls, filters, hellbanning, etc.) , but I feel like until now, I have taken the information access, discussion that goes on here and all the interesting people this board attracts for granted. I just don't see it being the same place to discus/mention ideas/concepts and ask questions if pg and co decide to stick with it, and it just becoming more watered down onanism that it can increasingly be and has been on track to becoming more of up until today. But this is the internet, and moments like these may inspire someone to offer other environments.
On another note: I'm finding it really fascinating to be able to experiment with social systems like this. I'm excited to see the posts of people analyzing the affect of a change like this via the search api or scraping.
It's funny, since we lost usenet 10+ years ago, we lost reader software that show which comments are new since you last time looked at a thread.
In this sense, the software we had in the 90's was technically superior to the web forums we have today.