I think it was the inability for GUI's to stay stable. Gnome went off the rails, Unity completely ruined Ubuntu[1], and KDE always felt very cheap and hard to navigate. My opinion, yes, but I always felt the GUI changes in Linux were extremely gratuitous after Gnome 2. Couple this with the fact that for a decade, the actual GUI was tied very, very heavily to the apps. So you had to use Gedit in Gnome, or whatever the…
Can someone please explain to me why everyone says that Gnome went off the rails? Gnome 3 to me was, except for leaving behind a lot of legacy systems, an extremely usable and downright pretty UI. Menu, search, windows, and virtual desktops all available from one keypress or one hotspot. I thought that was a stroke of genius myself.
I think more than anything it's good old nostalgia. The applications menu is no more, instead it's a grid where you have to search for what you want or whatever. There's a massive screen overlay instead of a nice little dropdown.
Multiple desktops was a good feature that's come with Gnome 3, though.
If I recall, perhaps some indication of the intentions of Gnome 3 can be seen by the fact that you are prompted to drag up (really?! on a desktop?!) in order to unlock after you've entered screensaver or something. So there could be some of the same reasons why people initially disliked the Win 8 view.
But mostly, Gnome 2 was just so simple and familiar, though I don't know if that's my hindsight or whatever. Point and click to what you want to run, put things on your desktop, do whatever. No BS.