This is pretty the sole reason I don't use gimp anymore and have no plans to go back, ever. I used it on OSX under X11 and had no problems with the mental gymnastics using control instead of command because, well, it wasn't GIMPs fault.

I was so excited when they made it a native app, too.

If Command-E actually brought the window up in front of the rest of the windows instead of hiding it behind the main window, it might have been a different story.

Just my two cents.