Aside from the issues mentioned (#1 up/down vote arrows too small
and too close together, #2 screen is too wide, which makes the text too small, #3 links are useless without copy and paste unless they are live or super easy to remember):
#5 When you click into the comment or reply box, the iPhone goes into a super-slow mode when trying to type. I found that if I can pinch and make it smaller, then everything works just fine. But, it's hard to do quickly because you have to grab space outside of the actual comment box.
#6 Flash. I
hate clicking on a link to be taken to some lame Flash-based site. Some kind of warning or flag or something so I don't waste my time. This would be nice on the desktop too, but it's quick enough that it isn't a big deal.
#7 The "home" page link is pretty hard to hit all the time.
#8 The comments link is often hard to hit (without hitting the story right below).
I do about 80% of my HNing on the iPhone, so any improvements would be huge. Thanks for looking into this, Paul!