Form factor dissonance for another. GNOME clearly targets the mobile form factor, and it fails me for all the reasons Metro in Windows 8 failed me because guess what: I'm using a desktop/laptop, not a tablet/phone.
I had issues with ubuntu's unity back in the day and I switched over to i3wm, but I didn't find I used tiling enough to make it worth losing the usability of a desktop environment
I think it's more fair to say all form factors are treated equally, to the possible detriment of focusing exclusively on desktop. I think Gnome does well and is really versatile no matter which form factor you use, and I didn't have much issue moving from Gnome 2 to 3, or Windows to Gnome, or OSX (at the time) to Gnome (I've gone back and forth a lot over the years).
For me, workspaces (which Windows lacked natively until very recently) and Alt+Tab/` are how I get around.
The customizability argument is a solid reason to dislike Gnome, but not for all time. Things do get better each release. Well, except for extensions, which always break.