I already mentioned the System Tray, back then I used MegaSync for cloud backups and that app was completely broken due to the lack of a Tray. (I have since switched to using Syncthing and an old laptop with a USB HDD as a ghetto """""NAS""""" solution... Which would probably work quite well on Gnome actually, as Syncthing is a service and is controlled through a web interface)
Wine stuff was janky as hell. As were Qt apps. For one thing wine applications, too, expected a Tray, and would instead spawn a tiny window at the corner for tray stuff. Plus there was weird behaviour with some windows and the way they layered. As for Qt apps? Gnome offered no features for setting the look of Qt apps, so if I set Gnome to dark mode (by the way, very neat feature how Gnome's default theme deals with that, no joke here, very seamless and elegant, even if I'd never use light mode willingly), Qt apps would still be bright and I had to just install a third-party application for it (qt5ct) and set something in my /etc/environment.
All of these things had solutions, to be sure, an extension for the tray, a third-party application for the Qt apps, etc. But then I did an apt upgrade and literally all the extensions broke. So I had to spend an extra hour that day figuring out what I'd do about that. Joy of joys.
Then there is the Gnome File Manager.
Why in the name of all that is unholy did it not let one type in the addresses of folders? Or copy them or... ? Sure, icons and breadcrumbs are nice, but being able to type in an address when you know it saves a ton of time. And maybe I want to copy a location to use it on the terminal? That should have been one of the first things to be implemented. Apparently a recent patch to Gnome has added the address bar "feature" (which has been part of Windows Explorer since 1994 and of every Linux File Manager I've known since forever--), but like. Bruh.
So I installed Thunar, the File Manager from XFCE, but now I was using a separate file manager entirely and having to deal with everything that comes with switching file managers from the DE's default. Like. WOW.