FTP is useful for bidirectional file exchange over the Internet. There are other protocols, but they all have drawbacks. SFTP can be used for similar functionality, but it requires users to have SSH access. SMB and NFS don’t really work so well over the Internet and are a pain to configure for multiple users. For setting up accounts dedicated to transferring files, you really can’t beat FTP (or really FTPS, which is just FTP over SSL).
Security-wise you set it not to run commands (and maybe chroot) and you're done, right? And difficulty-wise isn't granting SSH access very similar to FTP access?
I don't understand the issue.
But in the most common case a "system account" is a line in two text files, isn't it?