I researched the usability testing Gnome made, and I found only 1 related to Gnome3 but if you can point me to the study where they found that removing system tray is a good idea I really want to see how this study was made.
The truth is one more more Gnome3 designers that had the vision on how Gnome should look, that branding should be non optional, they did not know what XFCE is.
Sometimes, the problem is simply that some users really are using your software wrong. Not compared to how you think they should be using it—compared to how everyone else is using it, and so (via usability tests) how you're building it to be used.
Or, to put that another way: https://xkcd.com/1172/
Before you rebut: I'm not saying that that's true in this case. (I'm not saying it's not, either; I don't know enough about this case to judge.) I'm just clarifying the reasoning behind the general principle. People hate change no matter how justified and evidence-based it is. So inevitably, in a project, there's going to be some number of bug/issues filed where the underlying motivation comes down to "the user wanted to whine because they had to learn something new." It's not an excuse to ignore all user-filed bugs/issues; it's just an argument against people who insist that 100% of user complaints should be taken seriously. There is a "malingering quotient"—a certain percentage of complaints (different for each project) that comes down to people trying to avoid the work of coping with change.
See also, the Lizardman quotient: http://slatestarcodex.com/2013/04/12/noisy-poll-results-and-...