As with others, I'm not sure what you mean by pagination.

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