It would be very useful to have an ftp server, ala ftpii, running in the background. Something akin to XBMC’s background ftp service so you can move media around at will while Wiimc is running. Shouldn’t be to obtrusive or resource hogging to integrate.
Then I’d suggest you nag the wiiftp programmer to update his program. WiiMC cant do everything, it’s not like we have all of Microsoft behind this project.