I’m less inclined to attribute it to “these days”, as I remember the contemporary copycat themes in e.g. KDE and Tk looking off as well. Even Swing with the native look-and-feel didn’t quite look or feel right, IIRC.
As a (weak) counterpoint to supplicating ourselves to the old UI masters, I submit Raymond Chen’s observations from 2004[1] that the flat/3D/flat cycle is largely fashion, e.g. how the toolbars in Office 97 (and subsequent “coolbars”) had buttons that did not look like buttons until you hovered over them, in defiance of the Windows 95 UI standard. (Despite Chen’s characteristic confident tone, he doesn’t at all acknowledge the influence of the limited palettes of baseline graphics adapters on the pre-Win95 “flat” origins of that cycle.)
Also worth noting are the scathing critiques of some Windows 95 designs[2,3] in the Interface Hall of Shame (2000). I don’t necessarily agree with all of them (having spent the earlier part of my childhood with Norton Commander, the separate folder/file selectors in Windows 3.x felt contrived to me even at the time) but it helps clear up some of the fog of “it has always been this way” and remember some things that fit badly at first and never felt quite right (e.g. the faux clipboard in file management). And yes, it didn’t fail to mention the Office 97 UI, either[4,5]. (Did you realize Access, VB, Word, and IE used something like three or four different forks of the same UI toolkit, “Forms3”, among them—a toolkit that looked mostly native but was in fact unavailable outside of Microsoft?..)
None of that is meant to disagree with the point that submitting to the idea of UI as branding is where it all went wrong. (I’ll never get tired of mentioning that the futuristic UI of the in-game computers of the original Deus Ex, from 2000, supported not only Tab to go between controls and Enter and Esc to submit and dismiss, but also Alt accelerators, complete with underlined letters in the labels.)
[1] https://devblogs.microsoft.com/oldnewthing/20040728-00/?p=38...
[2] http://hallofshame.gp.co.at/file95.htm
[3] http://hallofshame.gp.co.at/explore.htm
[4] http://hallofshame.gp.co.at/visual.html#VISUAL36
[5] http://hallofshame.gp.co.at/visual.html#VISUAL38