Great plugin. I am really looking forward to watching it progress. One big thing that I think you should look at is how your plugin embeds code when some css is excluded. Example
<link rel='stylesheet' href='/wp-minify/min/>
<script type='text/javascript' src='minify/min/</script>
<link rel='stylesheet' href='/excluded css>
So what the issue is is that you embed css then js then css that was excluded. This is an issue because nothing will load parallel to that js file and it stands to believe it would be a large file. If you could make it so it loads minify css, then excluded css, then minfy js, then excluded js... we'd all be happy campers.
Additionally I read the post about identifying what js goes in the foot and I think thats a great idea too.