I too have a 1200S, and ScanQuix, and it works absolutely great! In fact, it works far far better than the Windoze AND Mac equivalents! The only problem I ever had was that I found out for the first time I had an old SCSI chip when I would scan in color and get scrambled colors.
The 1200U was USB, so I assume the 2000U is USB. I recently ordered my first Amiga USB interface from Software Hut and haven't recieved it yet, so I can't comment on that...