It would be nice if the emacs key bindings could continue to exist in GTK, but using some other key than "control." For example, the windows key is virtually unused and right next to the control key. I don't even know one application-- not one-- that uses the windows key for anything.
So we could continue to have these highly useful shortcuts enabled at all times, without conflicting with the keybindings set up by the application. This would also resolve annoyances like when I get used to the shell's control-W behavior, and type control-W in the browser.