One problem that has been around a long time, and is still present is that when you quit 'q' from ediff and the little frame closes, the focus won't return to the previous frame. Strangely, the decoration from the window manager is highlighted, indicating the window has focus, but the cursor is hollow and typed keys don't work. You have to click on another window (not emacs) then back to emacs to restore the focus. I'm seeing this on linux. Window manager is currently kwm (kde) but I'm sure I've seen this with others, such as fvwm.