What has been fundamentally broken in the comment system? Nobody seems to say, they just say it sucks, or is fundamentally broken, or as you say is an add-on, etc.
I'm not the GP, but I'll answer with the 2 most critical points for me personally.
1) the fresh user experience involves by default full expansion of 0 and -1 comments. This is pure poison. Much as I laud the side of the debate that paints us commenters as *contributors* rather than just 'audience', the fact is that there are as many poisonous comments as golden ones. Exposing new users to the site to all of those instead of hiding score:0/-1 by default and 1-lining score:1/2 will simply leave new visitors with the wrong impression of the site (IMHO)
2) for me, the ability to direct link to comments is critical. This seems missing, and as yet I've seen no promise to implement it in beta or keep its aspect of classic around permanently. For instance, I like to share specific comment subthreads, like this one, between myself and active duty US Navy Information Warfare Officer Dave Schroeder from 8 months prior to the Snowden revelations-
snippets of context include-
That's one problem with cyber (Score:5, Insightful)
Disclaimer: I am a Navy Information Warfare Officer.
First, it's important to note that the White House didn't confirm the suspected source. It was anonymous officials who said this appeared to originate "from China" -- take that as you will.
A couple of things:
1. I thought your Google manifesto was very good (I know it's a work in progress).
2. I think you're reading WAY too much into certain things. ... ... ...
Back to the other issues. I'm a little disappointed you called so many of my responses straw men; they're not in any respect.
I have not seen any serious calls for "backdoors" in secure protocols. You're completely misunderstanding what even the FBI wants: you're imagining a scenario where "the Man" has a secret backdoor to any running system, encryption, or secure protocol, anywhere. That is not only false, it actually would be gravely detrimental to our own security: we -- individuals, the civilian sector, the government, the military -- rely on the security of these protocols. It's similar to the belief among some that NSA has a "secret backdoor" ...