The ability to ftp the backup to another server using ftp details would be extremely useful. I would use this script to backup one website to another hosting.

Running the script as a cron would automate the above (I have read the earlier post - "calling backup.php?c=backupdefault")

Creating Profiles. It would be useful to have several backup profiles to call from the cron. For example:
backup.php?c=backupdefault
backup.php?c=backup_partial_file_system
backup.php?c=backup_database
etc.

This would allow different backups to be run with differing frequency (eg - Database every day, file system every week)

Have you seen MyBackup (http://www.tufat.com/s_mybackup_web_database_exporter.htm) - I was using it, but it is a bit flaky, that's why I am so happy to have found Idut