Re: About comments
Many commentards agree. See the huge feature suggestion threads. Although I've yet to come across any forum software that handles everything well. But it would certainly be nice not to miss out on conversations with people who've replied to you. And fully threaded forums would be far better.
As to your second point. There is a way of telling which post a reply is to. Not that it's by any means perfect. But if you click on the little grey swirly arrow thing on the left of the post, which is there to tell you it's a reply, it puts the post its replying to right to the top of the screen. Which I do in the most confusing cases.