I was an avid GNOME user from GNOME 1.x to GNOME 2.2. Like many other users (including Linus Torvalds), I became sick of what I perceive as an "anti-user" stance from GNOME. That is, they ignore their true users (most of the classic, Linux-using and UNIX-using crowd) for some mythical user that gets confused by options.
I'm compiling of specific transgressions so I can mention them easily in conversation.
How to turn off gnome-terminal's cursor blinking (Chris Siebenmann): GNOME makes it difficult to find the "Disable blinking cursor" option for terminals, making it more and more difficult to find.
Resetting defaults with GNOME programs (Chris Siebenmann): GNOME's gconf system (reminiscent of the Windows registry) makes it difficult to reset settings to their defaults, and is designed to accumulate cruft