Linux uses the File System Hierarchy which Windows does not use. How do I keep my system organized while keeping to the FSH.
Altogether it's actually not that different from Windows, it's just shuffled around a bit. You'll have your /home/yourusername/ folder, which is where you'll put most of your files. If you have more than one hard drive in your machine you can mount it under /mnt/ and then store the files on it as you would normally. You don't have to worry about where your programs are stored (your package manager will take care of that for you).

re: the command line
For the most part I agree, but I also think it's a solved problem. A linux install with Gnome is on par with Mac OS when it comes to user friendliness, with no need to ever look at a terminal in order to do things. The UX here is nearly a solved issue. However I also feel that "growth" or "mainstream success" is no longer something I feel like I need linux to achieve. When I started using Linux in 2009 half of the programs I tried were pale copies of proprietary software. WINE barely worked. Game support was almost non-existant. WiFi drivers were genuinely almost always broken. Flash forward fifteen years and all of these issues are fixed. Using Linux on a day to day basis makes me happy, I no longer feel like I'm missing out on anything by using it. That is such an incredible leap to take. The key takeaway is that all of these problems were solved without Linux becoming "mainstream". It and the community around it have just kept moving along and making it better over time. It's been lovely to watch it grow like that. A fully-featured and powerful terminal is just one part of this fantastic, open computing environment that I love.

As an additional note to this, I do think that Linux is poised to really take off among one particular demographic: PC gamers that build their own machines and can now finally see a good alternative to forking over $150 to Microsoft for their OS. The Steam Deck has definitely turned heads here. I don't think the legions of people buying laptops to take notes during university lectures and browse Facebook (the "20 wpm typers" out there) will be very interested in Linux machines no matter what we do, so let's focus the energy where it counts.

Not something that you asked, but please remember that most of the distribution managers know FAR more about the system than you do. If at all possible, be sure to follow the recommendations at DontBreakDebian (adapted to your system of course), to make sure you have a stable system.

That means things like avoiding whenever possible installing from random sources or changing settings that you don’t really understand. Whatever you do, don’t try to change anything about the kernel, graphics drivers, or standard libraries / shared packages unless you’re absolutely certain you know what you’re doing.

Windows has a filesystem hierarchy. It's super similar to the *nix filesystem hierarchy because that's what Microsoft mimicked with nominal differences.

/home/username is the same as \users\username

/bin is similarly what \windows is.

/sbin is \ProgramFiles

/etc is your windows registry. Only you can easily edit it with nearly anything. And it's generally hyper documented. Unlike the windows registry.

Gnome and KDE both provide fairly polished GUI for 80% or more of what an average user is likely to need to encounter. There is generally no need to sideload. In fact, the concept doesn't really exist. You are the system admin. You are root. There is no one to circumvent on your system but yourself. 90% of the software you could ever want will be within a distros repository. But these days you can download app images, flat packs, etc. That allow programs to be run on multiple different systems as long as they're binary compatible. Because those containers pull along all dependencies needed to run said applications. But even then depending upon the app etc you can still pull from other distribution, repositories etc sometimes . Under Arch. I have had things installed from the aur that turned out to be Deb files that it downloaded extracted and then dropped the files in the right place. However, that can only be done when required libraries are met. If the versions differ by too much. Which can easily happen between different versions of the same distribution, let alone other distributions. That won't work. It's like the missing dll files under Windows.

The Wayland xorg issues. If you need "just works" that's going to still be Xorg for a while to come. Though many distributions are moving to Wayland being a first class choice since it has come far enough. I have only had Wayland issues with two programs ATM. And only one of those is common, and the issue mostly cosmetic. Window decorations missing on Firefox. And that may be down to my chosen window decorations. The other is an obscure 3d game primarily made for Windows since 2004. That does have a Linux version. But under Wayland currently it goes seizure mode.

Linux already has mass adoption. (Servers) Desktop adoption is only a hurdle because of monopolistic anti competitive practices from Microsoft and Apple. A lot of that specifically due to momentum from Microsoft. They actively punished integrators that attempted to ship any OS but windows. And it's largely stuck around that way. A lot of the first party SI that still exists offer zero non windows solutions to home users to this day because of it. There are SI that do provide it. But they are often rather niche and fairly unknown. System 76 being one of them. It's very little to do with command line etc. Only when system integrators all start offering it as a general choice will the home user see much change.