The discuss / comments feature is potentially powerful but right now not terribly usable. Here are a couple of requests.
1. Show the comment count for each page.
If each link in the left menu of the generated prototype had a comment-count, I'd quickly be able to scan down and see where people have left comments.
2. Create summaries for prototype owners of discussion activity.
Perhaps a daily/weekly email, or a dashboard, detailing who left comments, on which pages. Saves me having to open the link daily to see who said what where.
Notableapp does this very well.
3. Onpage scribbling & commenting feature
I'd love for clients to be able to leave comments on the page, not just to the side.
See conceptboard, noteableapp, markup.io etc for examples.
4. Compatibility with existing onpage commenting
I haven't tested this recently, but previously I couldn't get my prototype to work well with 3rd party social commenting services like notableapp or markup.io. Probably because of the frameset.
Anyway, keep up the good work!