IMHO the software should be integrated. Think of it as rather like wikipedia's articles and their attached discussion pages, etc.

There can be layers of content and not everything on the site needs to be an article with comments, though it doesn't hurt if it is. The same article and the same comments can be presented visually in different ways. In fact, each ET diary and each comment are stored separately in the database, which links them logically and allows them to be displayed on the same browser page. The possibilities are endless when it comes to content and its presentation.

Personally, I think if content (including comments) could have a revision history and multiple people able to edit it, we'd go a long way towards achieving the flexibility we need for cooperative work.

We have met the enemy, and he is us — Pogo