I was wondering, have you planned to serve static files directly?
It's faster than loading WP for each kind of minified resources (CSS and JS).
It would be even faster on servers where PHP is loaded only for php files, not static files.
I'm not sure there is so many changes: you already build the output.
It may then be located in the wp_uploads_dir (it's assumed it already has write permissions), and served from this URL.
On each request, you still stat the called files, to check if the static file is older than the most recent resource.
What do you think about that?
I use this technique in my WP-LESS plugin (which generates static CSS files with LESS preprocessor), which enables by the way those files to be included in WP-Minify as they are considered as local files :-)