Now I have also played with it a bit more I have found it is possible to minify 100% (as of right now that is my opinion)
But I dont use W3TC and had to fiddle - so not an out of the box fix but possible. I used BWP Minify http://betterwp.net/wordpress-plugins/bwp-minify/
Very flexible for a reason = minify can blow!
Since developers typically dont want to hear this announced as a fantastic tip because then those who want to speed up site or save server powers (99%) start to give invalid bug reports and such I just give headlines. Based on a child theme with no load of extra skin.
In style.css of child themes remove line with import of main style.css
Deregister main style.css AND style.css from child theme (not 100% sure this is needed, should not with same handles I think but no harm done)
Enqueue same 2 style.css files (and again if handles are the originals no need to deregister)
Custom-styles file seem to work fine being stuffed in the mix more or less randomly. But one to keep eye on if things break.
Best way to deal with minify is to read that page from BWP. Hooks and code snippets. Coming version will be a bit more user friendly but if everything is ??? then dont minify. The way certain other tools present this is just wrong. Also remember than even if all functions/features/links on a site is tested and nothing can possible break you have to redo all testing everything a change has been made, like update to CSS and plugins. Not so sensitive once proven to work but in theory this must be done to be sure.
One of the weird changes I had to deal with show how crazy can be. I use a sliding panel (not from Suffusion) and it work ok with or without minify - with one exception. It has its own CSS file which I override in child themes style.css. Problem is when minified order of code/file load is apparently changed (or what ever) and I now have to be more specific with CSS declarations or use !important. 3-4 necessary lines are ignored when minified (sliding panel CSS come out on top), not an issue when not minifed.
I also expected problems with Suffusion bundle of JS code in suffusion.js and may be there are some. Drop down code works. Again, nothing has been proven to work with no testing so ALL features based on code in suffusion.js must be tested.
I think that plugin by far is the best, also dev!, but it would be cool if it could bundle with NO minification, like W3TC can. So instead of having to exclude each and every CSS and JS file when there is a problem, or 10, one can just go BAH and bundle instead. Biggest advantage of this is less HTTP requests anyway. Server can gzip and perhaps PHP cache plugin can help as well.