Firstly, I think that comments on stories have, for the most part (and so trolls aside), been a really, really strong addition to the site. I say that as both a reader and an author. As a reader, I very much enjoy finding out what others think of the story and if it matches my own thoughts or not. And as an author, I find them very, very useful feedback.
That said…
I'm currently reading a recently completed long serial. It's very long. 50+ chapters. And there are 33 "pages" of reader comments on it. But… The comments only appear at the end of the whole story. And as they are currently displayed in "reverse chronological order", it means that to read comments related to the chapter I'm on, I have to hop to the end of the story, then to the last page of comments and work my way back. Also, since the comments only note the date of posting, I have to open the story index to check the dates of the chapter postings. And even then, things might not match up.
Further, let's say that I'm reading "behind" the posting of chapters, or after the completion of the piece. If I wanted to add a comment related to, say, chapter 15 of 60, I can't currently do that without going to the last chapter.
So… My suggestion is this. Could comments be attached to chapters in serials rather than the story as a whole? Thus giving the reader an opportunity to comment on each chapter, giving other readers the chance to read comments related to where they are in the story, and giving the author even better feedback than the comments currently do.
I say again, I really like story comments. I think they are really useful. This is just a suggestion for possible "improvement". I don't see how it would be possible to implement retrospectively, but could it be done for new serials going forward?