My immediate thoughts were very similar to cperciva's. In the status quo, there's already a disincentive (for those who care about average karma) to comment on any posts that require scrolling down, especially if posts above them are heavily nested or if they themselves are. I can think of a particular discussion I had with a well-known HN user who has professional/financial incentive to care about his karma statistics, and as our two person back-and-forth got slightly too nested but very much unresolved, he merely liked my final comment and never replied.
If pending comments are applied to anything except the top-level, I could see this having disastrous effects on the quality of response in discussions since responses in low-traffic branches will likely not even show up.
With the availability of browser plugins and user scripts, I anticipate an "off-HN" application popping. Interested people can shadow the "canonical" HN discussion and continue a discussion that has legs, possibly grafting it onto HN itself.
Of course, it may be simpler to bot up a subreddit and do the same thing via convention. That may be the best result, redirecting the reddit-like dross back to reddit, where it belongs. Throwaway accounts will be mechanically discouraged along with the me-too, ya rite, and other useless posts.
Hopefully this will prove overly pessimistic. The way I see it, either we'll be proven wrong or pg will revert to the system we know and love until he comes up with a better method for improving the quality of comments.
I actually found it optimistic, in the "destroy a village to save it"[1] sense. HN, as it currently stands, will cease to exist. I suspect the volume of submissions pointing directly to old wikipedia articles will dry up. I consider this a good thing.
I suspect the volume of submissions that are reposts piling onto something already on the front page (Erlang, Erlang, Erlang, Erlang, Haskell, Haskell, Haskell, Go, Go, Go, Snowden, Snowden, NSA, Erlang, Lisp, Lisp, Lisp, Lisp-flavored Erlang, NSA, Erlang, Erlang, Bacon and Spam, Javascript, Framework, Framework, NSA, Erlang, Haskell, Haskell, Erlang, Lisp, 2048, will dry up. I consider this a good thing.
I suspect I will spend less time on the site, either because conversations will become static expressions of views or because I won't have to filter through as much content, even though much of which marginalia I find quite engrossing. I consider this a good thing.
What comes next is open to conjecture. It could be a more mature salon full of reasoned discussions or it could become a ghost town with lots of great, old, discussions.
If pending comments are applied to anything except the top-level, I could see this having disastrous effects on the quality of response in discussions since responses in low-traffic branches will likely not even show up.