I also prefer reading threaded discussions, but are you aware of a good way of keeping track of new messages? That’s my main issue with threaded discussions, for example here on HN.
The way Usenet clients and traditional email clients work is that unread messages are marked as such (usually by use of bold typeface), and you have keyboard shortcuts to navigate from one message to the next, or to jump to the next unread message.
For example, the Tab key jumps to the next unread message, Space/Backspace scroll up/down within a message, and the Up/Down arrow keys jump to the previous/next message (regardless if unread or not). A message is marked as read automatically when you navigate to it (it gains focus). There’s also a keyboard shortcut to mark a read message as unread again if you w.
The keyboard navigation means that only one message has focus any point in time. You have a threaded view of all messages, where the unread ones are highlighted (e.g. by bold typeface). Then you can decide which ones to navigate to. Usually you just use Tab and Space to jump/scroll through the unread messages. It’s incredibly efficient to use.