Asset combining follows fairly naturally, should we need it. It is also rather trivial to output js inline instead of referencing js files for development purposes.
I'm thinking #1 could be implemented via a new template tag.
not sure i really understand your logic to clarify
#1 would work perfectly with my proposal,
#2 makes no real sense too me why do we need both , still makes no sense to me to include in header if the JS is handled the right way.
#3 is where i get confused with what you are trying to say. Are you saying that it is trivial to remnove/externalize the JS from the template files or give them their own director/template file?
I have been doing front-end development for going on 11 yrs now and every project weather it be stand alone site, cms generated, or application theme and have always followed a strict seperation of effort for the file structure
JS, CSS, & images have always had their own file this makes working with, updating, replacing the theme extremely easy as you go exactly where you ned to to edit specifically what you want. I have never really understood PHPBB's idea of a file structure for their themes it has always been convluted and confusing from a developer mind set let alone the average user.
calling the css folder theme is one as well as including the image folder with in it but why do we not encapsulate the js files as they are seperate from the template it self after all JS is an enhancement not a part of a template, further more if you really want to get nitpicky the en folder should really be put within the images directory.