I've previously mentioned the GNOME "hot corner" issue that came up in usability tests. I'll admit that I still run up against this problem. The "Activities" menu looks like a clickable item to me (and it is, if you don't activate the "hot corner") so when I try to use the menu, my natural desire is to click it. But just as I go to click it, my mouse cursor activates the "hot corner." So when I click (a split second later) the menu closes.
This is irritating, to be sure, but it's not the one thing I would change to improve GNOME. It's something I can work around. Changing that one little thing won't significantly improve GNOME's usability.
Instead, I would relocate the "application icon" menu into the window it's associated with.
My issue with the "application icon" menu is that it's disassociated with the window it controls. It's not too bad on a laptop or any system with a single display; in that case, the "application icon" menu isn't too far from the application's window. But at work, I use a dual-display setup; my laptop is the first display, and my 22-inch external monitor is my second display. I do all my "small screen real estate" functions on the laptop screen, including Rhythmbox music, the terminal, and the file manager. And I do all my "big screen real estate" functions on the big screen, such as word processing, spreadsheets, email, and web browsing. The "application icon" menu icon loses its association with the application window when they are separated on different displays. As a result, I often forget that menu functions may be located in the "application icon" menu.
To improve this, I would move the "application icon" menu out of the top bar, and into the application window. Here's a simple mock-up:
|Mock-up of gedit, Nautilus, and Terminal; based on GNOME 3.10.3|
I'm no graphics designer, but I've done my best to represent visually what I'm trying to describe. In this mock-up, GNOME's top bar is reserved for GNOME interaction: the "Activities" menu, the date & time, and the wifi & volume controls. The "application icon" menu gets moved into the active window. This provides a stronger relationship between the "application icon" menu and the application itself.
Actually, I cheated; I changed two things. In moving the "application icon" menu into the window, I also added a slight highlight to the active window. But that's a minor change.
Edit: I just realized that when I created my mock-up, I accidentally removed the "×" in the upper-right, to close the window. That's an error.
In this mock-up, only the active window has the "application icon" menu. This is intentional. That's one other way that GNOME would highlight the active window. And by having the "application icon" menu only appear on the active window (and disappear on inactive windows) the user would be more likely to notice the "application icon" menu, and thus draw a connection between the "application icon" menu and the application window.
Importantly, the "application icon" menu retains the downwards-triangle, which is a hint to the user that the menu is clickable. It's revealed to be a second menu. And menus are important; if the user cannot find the function he or she needs in the regular menu, they would now be more enticed to try to "application icon" menu.