Check the latest offerings from Alpine. They claim to offer high quality USB connections capable of working with thumb drives - hard drives and all usb mass devices including non-ipod "mp3 players."
I noticed these on their site recently and was refreshed to see someone is once again looking at doing high quality connections using hard drives. I've been using a digital media player through its optical output into my DRZ9255 for about a year now and it works great, but requires a separate monitor and can't be controlled by the head unit in terms of song selection. It works, but the wave of the future imho are head units with built in hard drives or at least connecting s to hard drives up to 500gb+.
I have to tell you, not having to sort through hundreds of CD's to find the song you want - and still getting very high SQ is really nice =) Your solution may be here now, but if not, its not far off!
The headunits that have USB need to be compatible with various playlists to be truly equal. Without that I won't be buying one. I have no way so far to confirm if any given HU will be compatible with playlists stored on the hard/flash drive.
iirc the alpine models said that they ignore all none recognized file types, but do recognize playlists and various music file formats. Not hard to confirm when they they post their manuals online for you to browse...