We have put some more love into duck, the CLI version of Cyberduck. There are now several new options to facilitate automation jobs.
--retry <count>allows to repeat failed connections.
-ywill dismiss all prompts and warnings with Yes by default.
--throttle <bytes/second>allows to throttle transfers.
plus the most interesting to improve throughput is
to open multiple concurrent connections for transfers (#1135). For downloads, larger files will be segmented into multiple parts (#4498) to transfer with multiple connections and assembled again when complete. This feature will also find its way into version 4.7 of Cyberduck.