I agree that using FTP by hand can be very frustrating. It is difficult to ensure that all your users are consistent with naming etc. But most of the problems you have using FTP directly would be present in some way with any direct copy method (file share, or even webdav).

I believe that in the FHCRC proteomics lab someone wrote some simple scripts in the distant past to handle this. So instead of copying directly the users run a script that ask the right questions copy the files and verify them.

In 8.1, we are introducing a new feature for copying files to the server that makes "dropping" a directory of files to the server easier. You would navigate to the place in the UI you want to put your new run of FCS files say. Then hit the "Upload files (ftp)" button. Now you just browse to the directory you want to copy (or just drag and drop it).

This is just one step, and I hope to continue to improve the user scenarios. I don't think the underlying file transfer protocol, however, should really matter.