Companies like IBM and Microsoft did a lot of HCI research back in the 80s, and made a lot of progress with usability and common idioms that all software followed. Then when displays with 256 or more colors became common, all that went out the window.
All those Windows Media Player skins were awful because they used so much screen real estate on dead space. Whereas the plethora of Winamp skins kept the economy of screen real estate while still providing unique and imaginative visuals.
The whole skeuomorphic trend starting in the mid-90s was similarly awful for the same reason. First, it was often hard to tell what was a control and what was just decoration. Second, it often took trial and error to figure out what was what. And, as I mentioned above, these designs almost inevitably wasted huge chunks of screen space on decoration that provided no functionality.
Of course, we have the opposite problem now. All windows look the same. Title bars are mostly gone. And since companies like Microsoft replaced all their HCI experts with art-school dropouts who think the "flat" look with low contrast is cool, not only can you not tell what app you're looking at. Half the time you can't even tell where one window stops and another starts.
The only good UI thing that's come out of the last decade or two is a near universal support for "dark mode". Otherwise, I would greatly prefer the Windows 2000 "classic" look, or something similar.
I agree with your sentiments, but not your timeline. The mid-'90s was the high point for GUIs, with Windows 95 nailing it pretty much across the board.
And as you note, "flat" design is NO design. It's total dereliction of the design task. Fortunately we're seeing some steps back toward legitimate GUI, where controls are occasionally demarcated as controls.
A great example of Windows's pathetic regression is "dark mode." Since the early '90s (and I mean '91 or '92), you could set up a system-wide color scheme. Inverse color schemes were an unfortunate vestige of the late '80s, early '90s... the advent of the Mac, "desktop publishing," and the effort to make the screen an analog for a piece of paper. That analogy fails.
The result was millions of people reading black text off the surface of a glaring light bulb all day, every day. The first thing I did was set up a charcoal theme in Windows, pretty much exactly what all the "dark" schemes are today. And all properly written applications inherited it and all was good.
So... just in time for people to realize that this was the way, Microsoft REMOVED the color-scheme editor from windows. Only to have to hastily slap a hard-coded "dark mode" back onto the OS. So damned stupid.