Actually the GUI-fication of Windows Server was one of the many reasons Windows based networks are so insecure and poorly configured. It creates this notion that any "kid" can configure a Windows Active Directory Domain, and small to medium sized (and sometimes larger) companies hired amateurs to save a buck. I met some pretty bad sysadmins in the last 20 years of my life, who left a horrible mess wherever they lay their hands.
Not to mention that the GUI kept changing every year, because that's just how Microsoft does stuff; anything you learn becomes obsolete a year later. They are very volatile like that. This is not so in the Unix world, where API's and tools are kept minimalistic, are cleverly crafted, slowly improved upon, with stable releases coming out every few years instead of betas coming out every month. Indeed, history shows that a Unix person retains his knowledge for decades. Show me one Windows person who can say that what he learned about Windows 2000 Server is still useful?
Enough with the Microsoft Bashing, here's one product I actually liked that took the CLI forward: Splunk. They took the CLI and put it in a Web browser! Splunk is basically a data collection tool that pipes everything through whatever you type into the web based "CLI" prompt, with the basic function being a combination of "grep", sed, awk, with powerful regular expressions, etc.
The beauty of it is that you can take your piped processes, and save them as a "View", and you can even create charts based on the resulting data. The result is a Unix admin's dream dashboard into the depths of his IT environment. I seriously recommend any Unix head look into that technology, especially considering the product has a free version (the free edition removes some "enterprise" features, but for many applications you won't miss those features at all).
I also like the combined approach: UI tools that produce either scripts or configuration files that you can read and understand and modify manually if you wish. Make a change in the configuration file? It will register in the UI. Made a change through the UI? It will register in the files and scripts. You get the best of both worlds this way.