One of the more frustrating bits for me is that on OSX there are four modifiers (shift, control, option, and command), but none of them is exclusive to interacting with the "window manager". There's a lot of interface dissonance when I interact with anything over ssh (because "cmd" takes the place of an "alt" key), or use X forwarding.

I've dedicated Mod4 to interacting with my window manager for over a decade and it's sensible. Mod1 and control (and, if absolutely necessary, shift) are plenty for keyboard shortcuts for apps.