So the other night I was playing around with PortablizeMii. It is such a pain to migrate between memory card and USB/SD. GCMM is open source. I had a look around at the source and it should be possible to do a custom build of the app that would allow you to cut out the use of a PC altogether.
Basically another option could be added onto the GUI that would allow you to dump individual RAW saves onto the USB from the memory card rather than just one. I could probably even make it specific enough to where it exports it to the saves folder so that no moving of files is needed.
I'll take more in-depth look at this when I get to work today and report back later.