I don't disagree with your points (well 1 and 3 anyway) but you can't just ignore the major advantage of threaded discussions: that you can branch off into different directions without derailing the thread as a whole. For example this entire subthread is about forums in general and now about hierarchical vs. linear discussion - if you actually wanted to talk about phpBB (the subject of this thread) then with a linear view you'd have to sift through and enless supply of unrelated comments. Here you can just collapse subtrees that go in an uninteresting direction.
I also don't think your problems with threaded discussion are unsolvable. I've not seen any forum implement this but I don't see why you couldn't allow someone to reply to multiple comments at once. For display you'd show the reply under the topmost parent and then only a link (or pre-collapsed comment) under the other ones.
For updates, Reddit solves this by highlighting new comments since your last visits (or other previous visits you can select from), which works really well - except that they limit the feature to paying users and subreddit moderators. HN doesn't have that feature presumably because HN doesn't want long-running discussions.
For (2) Reddit (or RES anyway) also has a solution: hovering over the [parent] link shows the parent post.
The clutter vs. minimalism is an entirely separate issue. While I wouln't advocate for giant signatures, I think some customization (avatar, titles, etc.) can be important for community building.