The biggest frustration I've had with WordPress is the inability to remove the base category from the url permalink structure. The irony is that I'm very interested in using WordPress as a CMS, and its WordPress Pages -- a CMS "feature" -- that prevents the use of a logical permalink structure. Kill Pages and force me to create a category for static content any day over this mess.
If one mixes categories with pages, one comes up with a really illogical url scheme:
http://www.site.com/category/typing/
http://www.site.com/about/
http://www.site.com/category/forsale/
http://www.site.com/intro/
Huh?
To make matters worse, depending on the browser (I've seen it work sometimes), going to http://www.site.com/category/ will result in a 404. Going to http://www.site.com/typing may or may not also result in a 404 (again, I've seen it work occasionally).
It seems to me that there is a simple solution. Allow the user to turn off Pages. Without pages, there should be no need for the base category prefix. Those that like Pages can continue to use them, those that don't can ditch them.
I actually tried to switch to Textpattern over this issue. But Textpattern is so backwards in so many other ways that it just wasn't worth the heartache. WordPress is great software, but I think removing Pages would make it 1000 times better.