It's difficult to nail down specifics but I do agree with the gist of your post. Whenever we upgraded from our Snitz forums to CS the vocal majority have stated their dislike for the "new" forums. I've done 8 community sites (1 is actually 6 sites using the same community area) and it's been the same. Personally, I consider myself a forum junkie cause I spend a lot of my free time on a lot of gaming related forums. I can't help but compare my experiences there with our Community Server sites and I find myself disappointed.
My opinion as to why the forums aren't that great in Community Server is that I feel that the Community Server team just doesn't use them like the rest of us.
For one, some of them don't use the web interface and use the subscription service or newsreaders. So for those people they don't deal with all the UI issues that the rest of us do. It's apparent when you see posts posted / quoted via email. Also when posting about a bug sometimes they have no idea as to what the issue is because again, they don't use the web interface. It's not until a screenshot is posted that they have an idea.
Second, many of them use the Blog and Gallery for their personal sites so they have a lot invested in those aspects of Community Server. So you'll see those areas get a lot of attention and discussion. There is always a lot of neat things posted as to all the different things you can do with your blog. Not that that is a bad thing as Blogs are popular but a tad frustrating when the main reason your using Community Server is the forums.
Third, I have to wonder aside from the Community Server forums, how many on the team actually have experience with managing / running forums with a medium to large size and active membership. Actually, I should rephrase that... forums which don't cater to the technical saavy by which I rule out the asp.net forums as well. It's a very different animal when dealing with a community where it's members aren't programmers, web designers, or working in the IT field.
Then there are things like the not showing the post author, views, a last post column, jump to first unread post, no quick reply in the footer (people just don't get the quick reply modal feature and why you have to reply to a post vs. the thread) to name a few things that always come up. These are features people want but yet for whatever reason they're not there. Granted you can make modifications to add some of it in but these are basics that I feel should be in from the start.
I apologize for the wall of text and not summarizing w/ a powerpoint presentation with nifty bullet points. It's just that I really like the software but I get so frustrated at times because I know it should be so much better than what it is. By that I mean it's amazing on the technical / engineering aspect, the administration aspect of it is better than what I've seen in other packages, but the public interface is where it's lacking and unfortunately that's what all of our members / customers see when they visit our site.