Personally, I always use rsync for these sorts of jobs. Works over SSH so don't need anything on the server except SSH, if the trasfer gets interrupted it will resume from where it left of. Overhead from SSH is pretty minimal, but if you really want thigns to go as fast as possible, you can setup an rsync server ...
If you don't want to use rsync, just use SFTP or SCP.
I... think the only difference is that potential eavesdroppers could determine the number of files, and their rough size. And I guess... the filesystem location on the target server. I mean the main thing that'll be unencrypted is the FTP headers, so whatever else is in there.
The difference is small for the transfer of large files. The main difference is that SFTP is built on SSH, while FTP is built on TCP, so FTPS is required if transmission encryption is required.