First, the standard Cygwin-setup utility takes command line arguments that will avoid all of the prompts, so you can have a single command to update a system without having to do a lot of clicking. See this blog post from Cody Dunne.
Put this in a batch file, run it as administrator:
Or if you are typing it by hand:cd C:\cygwin wget -N http://cygwin.com/setup-x86.exe setup-x86.exe --no-desktop --no-shortcuts --no-startmenu --quiet-mode
Second, there is a nice command link apt-get like utility, called apt-cyg. It's a neat, simple bash script. Nothing to really install. Provides command like search, and text access to the list of installed packages. apt-cyg is in Stephen Jungel's github repo.setup-x86 -nNdq
Note: the key data is in the setup INI files stored in cygwin-pkgs/mirror-name/x86/setup.ini.
Hope this helps,