The most long running desire about this site has to do with the way comments are presented. I'm happy to report a fix for this issue. Over the weekend I stumbled across a configuration page I hadn't discovered before and there was a setting to change display of comments between "flat" or "threaded". The site is now configured to display comments in a flat arrangement, with the newest comments added to the end.
It's clear the majority of us want it to be this way.