I'm pretty sure this is intentional in order to avoid shallow discussions and not grab too much attention. I actually like this, but I agree with you that it can make it harder to get answers sometimes and you do miss some replies on especially older comments.
Not sure what you mean by this, the lists of posts are very obviously paginated, as (admittedly a bit awkwardly) are larger comments threads. Maybe you mean auto-scrolling pagination?
> No notifications on reply, so it's difficult to get answers to clarifying questions (/threads helps but isn't it).
While not a HN feature, there is a simple solution - http://www.hnreplies.com/
The lack of response notification is a feature, though yes, it can be annoying, and I find the degree to which comments or questions go unresponded is ... disappointing. That said, notifications abuse by modern Web / App systems is rampant. I'd like some sort of middle-ground, perhaps a responses / notifications link which would consolidate these. "Threads" is the closest there is to that, though it includes all a person's comments whether (newly) responded to or not.
Mobile experience is pretty poor, agreed, though it's sufficient for reading logged-out (my preferred mode). Composing text on mobile devices is a category error.
Deep threads (and greyed text with downvotes) is a very intentional site design. pg's discussed that in the past, see:
"What I've Learned from Hacker News" (2009) <https://www.paulgraham.com/hackernews.html>
Discussed at the time: <https://news.ycombinator.com/item?id=495053>
And four years ago: <https://news.ycombinator.com/item?id=19210923>
Some of the site styling can be overridden with CSS. I apply the following on desktop:
Dred's HN CSS Madhackery: https://pastebin.com/gLXiqKyd
There's also a dark mode I've created:
Dred's HN CSS Madhackery -- Dark Mode: https://pastebin.com/6PF3dCXH
No way to keep up with new comments on a post (Reddit doesn't have this either).
No notifications on reply, so it's difficult to get answers to clarifying questions (/threads helps but isn't it).
Ever-increasing indentation makes deep threads hard to read.
Generally hard to read and hard to click on mobile.
None fatal, but also none particularly tough to fix!