After more tests and research it seems the best two options for the WordPress admin are either minifying all scripts and loading most in the footer or concatenating and compressing them on per page basis.
Minifying and loading scripts in the footer gives slightly slower performance with both cold and primed cache and would depend on the ability to set appropriate caching headers on the server. On the plus side this method would be compatible with the current plugins and wouldn’t introduce higher server load.
On the down side the loading speed improvement with primed cache would depend on the availability of mod_headers and/or mod_expires (presuming most installations are on Apache). It seems many hosts have either one or both modules installed but that still leaves a lot of installations without proper caching headers. In these cases the browser would keep checking for updated content which would increase the loading time with primed cache considerably.
Concatenating and compressing all scripts would give better speed improvement and we will be able to set all needed headers. The last couple of days I’ve been testing a method that uses a separate php file similar to how the Gears manifest is produced. This is the same basic method used by many “website php compressors”, a stand-alone php function that gets as argument the names of the needed scripts then concatenates and compresses them. It doesn’t use server side caching (that proved to be problematic on some servers) since the cold cache page hits on the admin are relatively few.
The advantage is that WordPress is not run second time on every cold cache page load so it uses a lot less server CPU time and memory. The disadvantage is that it would work only for the default scripts whose paths are included in the script loader. This also seems to be compatible with all existing plugins as any additional scripts are loaded after the single script and all requirements are satisfied.
Another disadvantage is that a few hosts seem to compress all php output in a non-standard way that may result in double compression. This method would also need “Optimization options” screen with a few checkboxes that would allow the user to enable/disable the concatenating and compression as it won’t be needed when using Gears.