This is probably a long shot but I have a situation where most of the hosts I access are one or two jumps away from my machine, meaning I use ProxyCommand in my .ssh/config to make access far less laborious.

It would be brilliant if Cyberduck would eventually support this. An example of my config to get to "secure-host" via "bastion-host" looks similar to this:

host secure-host
	ProxyCommand ssh bastion-host -W %h:%p

If the proxy host is capable I use the -W flag, otherwise I use netcat.

Additional to this supporting hostname globbing would tie in really well, allowing configs for accessing multiple hosts, secure-host-a and secure-host-b like this:

host secure-host-*
	ProxyCommand ssh bastion-host -W %h:%p