Replying to myself?
* get rid of misc/ - in favour of - sites/all/themes/all/js - sites/all/themes/all/css - sites/all/themes/all/css/images the disadvantage of this is the directory depth both to type and to see in browser, the latter can be remedied in code It just occured to me that http://drupal.org/node/13095 will be made trivial in this case. Which will probably as well reduce the drupal.css hit on webhost traffic.
Earlier I made an experiment with splitting the drupal.css file into logical (for me) parts - color.css, framing.css, typography.css, icons.css and would say that it improved the maintainability and theme development. It was easy to find what do I want to change. Maybe it's me, but it is definitely a nightmare reading/editing/understanding huge stylesheet files. So implementing if xyz.css is not in my theme directory then load the default xyz.css will work fine. As a plus it removes redundant css code, simplifies the css dependencies, removes the need for dirty css hacks to override drupal.css defaults. The negative side is that a designer will always need to start with a copy of the default css file.
* */vendor is a worthy contender to consider - this way we won't mix drupal and non-drupal code too much - this will be easier to upgrade but otherwise I don't have an idea on all implications
* Although I use something like the suggested public/private separation already, I would NOT make it the DEFAULT - it is not for the faint hearted, it needs an installer for the majority of people. I have sets of shell scripts to do the maintenance here, but for an average webhost that is not good. It can be implemented with an installer.
* I wouldn't touch the css bundling with modules now - it is too complicated to achieve, but I would put it in the longer term TODO - having all css files in one location is logical, it is easier for the designer, it will be easier to handle within the theme engine the selection of which css files to include - for example a custom event.css for your carefully crafted theme- How would you do that with the current layout?