Okay, one thing that's really getting me... I'd love to see Comments for articles also have an extra database field to link to a WordPress user's user_id, if they post whilst logged in.
In this way it is easy to see if a comment is from a registered user, or an anonymous user. It goes a bit further. I would like to be able to highlight any posts that I make on my site, but as I use my first name (Mike), an anon user can also post with that name. I do not want to disallow this, but I do want to be able to separate my posts from posts made by anon.
A huge bonus for this could also be pulling the user's name from the DB. At the moment the name is stored along with the comment every single time you post; If you change how your name is displayed it will not retrospectively update old names unless you manually hack the DB.
I know there's probably argument for "oh, but if you store the name in one table then it's less db calls"... but I'd rather have more functionality and abstraction than flattening everything :)