I really do enjoy HN's design. But the fact that read stories become grayed out hurts in one circumstance: when you've started participating in a discussion on that thread. It would be nice (though admittedly it would break caching) if at least the 'comments' link changed color or were 'called-out' for the threads in which you have commented.
I'm not sure if you're aware of the [threads] link at the in the HN navigation, but it shows you all your comments and threaded replies. I use that feature to check back on discussions I've participated in.
Even so, I as a user who comments quite infrequently will often times want to, after reading an article, look at the discussion about it. On an almost daily basis I have difficulty finding that link because it has been so heavily obscured.
On long threads it usually becomes difficult to determine who a particular response was directed to.
There is no way to differentiate quoted text in your response.
The size of navigational elements are particularly small and hard to use on mobile devices.
You make the point that HN has clear brand identity, but that isn't much of an accomplishment. HN sticks to a four color palette ( Orange, Tan/Bright Desaturated Orange, White, and Black ), and places the YCombinator logo at the top left.
As someone else said, I think you are being far to critical. While I personally don't like the design of the site either, I wouldn't begin calling HN a good example. Sure HN is functional, but that is only one aspect of good design. Functionality in and of itself really isn't that difficult to achieve. It is when you are able to strike a balance between expressiveness, beauty, and functionality does a design become good.
