My understanding was that the Drupal core CVS repository would have everything under /public_html, and that the Drupal core tarball would have the same (this is how it is now). Why would you want to change this? Doing so would only confuse people.
Agreed. If we go ahead with this, the directory structure in CVS should match the structure in the tarball. If not, we're asking for trouble, and it is a nightmare for people using CVS to maintain/update their sites. My suggestion would be to keep the core directory structure as is for all of the above reasons and to provide flexibility for different packagers. Changing the CVS layout will cause a lot of trouble most notably history loss.
The real solution for ease of installation and maintenance will, hopefully, come with the installer Adrian is working on. He said it is his priority to make its appearance as soon as possible. With him we are working together on modules, themes and theme-engines (package) dependencies, and ways to package and manage those. A solution like that allowing your preferred directory layout will meet the 'cleaner directory structure' goals. In the end cleaner depends on the context of installation - shared hosting, hosting provider like Bryght, dedicated services similar to what I run in house, local policies ... Over the weekend I can prepare a patch for my earlier suggestion. It doesn't solve all issues, but at least it goes some way towards allowing a more flexible layout. Maybe we could prepare a couple of scripts to modify the directory structure to some of the usage scenarios. I wouldn't like to modify something which works and has it's merits for a simple but not all encompassing convenience.