For a fully featured revamped Permalinks control panel. Maybe even renamed to a URL manager or something to that extent.
A lot of times one of the things I spend the most time with wordpress sites is in the permalinks section, trying to figure out why my seo-optimized /%month%/%postname%/ tag or (anything similar here) keeps showing up a 404 not found page in the front end of the page.
I have looked to this fix: http://www.kevinworthington.com/how-to-fix-permalinks-in-wordpress-when-all-else-fails/
And it has worked a decent amount of the time, but for my latest example today I have a wordpress install on the main directory of a site, and another wordpress install in a sub directory, and wow does that not like to play nice.
There's got to be a way to make this better, maybe not revamp the whole thing but obviously we are all open to suggestions here.