Exclude some dirs from site backups or backup GS only

[yojoe]

I don't see a problem.
Only thing you have to backup is /data directory.
If you need to migrate to other host, just install a fresh GS instance with all plugins, and unpack /data from backup. Nothing more to do.

But if you need to create a custom backup, then prepare a small php script, and call zip packer with exec command. There are dozen ways of creating and maintaining backups, and since you need a heavily customized/sophisticated methods, then built-in GS solutions doesn't meet your requirements.