> while Ctrl is the modifier used at an application level.

DE features don't matter at all outside of cmd-tab and whatever the equivalent of spotlight is. The application level is the main modifier, and changing them all to cmd is essentially impossible at this point. A detail Haiku got just about perfect, I think.

Either way, ctrl as a gui modifier is a dealbreaker for me. It also breaks the use of readline keybindings for text entry.