One of the annoying things that we had for years with Drupal is that the directory structure could be much cleaner.
A better directory structure helps with a lot of things, such as backups and upgrades.
I proposed issue #22336 to address this issue. Over time, it has developed into the quintessential bikeshed issue, with discussions in that issue trying to do everything at once, and forking the discussion into other areas as well, and we end up accomplishing nothing for almost 5 full years now.
My goal is simple: Only index.php, .htaccess and robots.txt need to be in the DocumentRoot of a site. Everything else that is core goes into its own directory called "core" (or "dries", "axl" or "stan", I am not hung up on a name). We have another directory called "sites" that contains all site specific stuff, whether it is modules, themes, or files.
My proposed presentation is attached below this post as a PDF.
And while we are at it, please check Djun Kim's Drupal's Code Stats proposed talk for the core summit. I too feel that we are becoming more complex, and I am firm believer in simplicity. See my comment on Djun's blog as well.
My email signature for the last few years has been this:
Simplicity is prerequisite for reliability. -- Edsger W.Dijkstra Simplicity is the ultimate sophistication. -- Leonardo da Vinci
I hope that Djun's talk makes it, even if mine doesn't ...