My 2 cents…
Intelligent way to incorporate custom post types and pages into the RSS feeds.
URL structure with ability to modify based on post types.
Both of these 2 ideas are the most asked for from clients and about. I believe with the 2nd item WordPress would see a massive migration of older site to a WordPress based platform. Right now far to many stick with outdated monster mess code because they are afraid of URL changes.
I have been able to custom code site very simply to allow any and all content to be listed in the RSS feeds. It is a pretty basic ‘hack’ and would be easy to include in the backend with a select box style setup in settings.
I have been able to make custom URL structures for clients to move to WordPress on many occasions as well. I do believe there would be a great deal of flexibility if the permalinks settings had just a few more options. Perhaps an extra box with ability to add more to set things similar to taxonomy.
Just my 2cents worth of input 🙂