The intended purpose of this topic doesn't so much seem like Windows vs alternatives as it does gui vs cli. Not too difficult a mistake to make, most people don't even know there are alternatives to Windows, only that we've gone from command lines to Windows. I make liberal use of command lines in both Windows and Linux, but a lot of things would be a bitch and a half without a gui.
You can do a lot of things faster, easier, and better with a cli if you know what you're doing, especially in Linux where it's much more powerful, but there are also things, multitasking, for instance, that are much better left to, or impossible without, a gui. There is a place for both, and I don't think either of them are going anywhere too soon.
Unfortunately, most people are afraid of command line interfaces. I personally love the minimal simplicity of it. No windows, no buttons, no distractions. You tell the computer what to do and it does it. Every possible option you can do with the machine is at the tips of your fingers and depends only on your knowledge and typing speed.
My dad was afraid of the MS-DOS prompt and would freak out and get angry any time he saw me use a prompt or shut down into DOS to play a game. He had no idea what Linux was, and nobody I've met knows anything about command lines or Linux. I don't know a lot of computer savvy people, most people only seem interested to the extend that they need for gaming.
I don't know as much as I'd know if somebody could have taught me, but I've been able to teach myself a lot over the years through books, websites, practice, and so forth. There's really nothing to be afraid of when it comes to cli, and no reason to hate on gui.
I appreciate that, with old computers, it didn't take too much to know all the ins and outs. The C64 came with a manual covering all of the commands you could use, and you could learn pretty much everything from the programmer's reference and other books. I loved this, and it played a significant role in genius game designers learning all about their machines down to the hardware level and write very efficient code without the benefit of libraries and other modern conveniences such as wildly varying hardware that has power and memory to spare.
Today, nobody uses WIndows help, and it's pretty useless besides, with troubleshooting no better than your average tech support and minimal information. In Linux, you have man pages and whatnot, but those aren't helpful for absolute beginners, and for both, it can be hard to figure out where to even start learning everything you might want to learn.
Computers have become more complex. They've also become tools that are useful to every one of us. This was inevitable, and neither Windows nor gui's are to blame. Unfortunately, becoming computer literate has become more difficult than ever, it's difficult to get a foothold. There are plenty of websites to learn things, but knowing what it is you're even looking for, and finding a place that can actually teach you well, can be more than half of the struggle.