You should look into kinto, it completely remaps the modifier keys system-wide and worked pretty well when I tried it (I switched to i3wm so I use super for i3 shortcuts now)
Ooh, that's really cool. I hadn't even thought of dynamic rebinding as a potential solution—it seems a little more hacky than proper native functionality (especially since application menus will still display the CUA/Windows shortcuts), but it sounds like a great way for people used to Macs to comfortably use Linux and Windows. Thanks for sharing!
https://github.com/rbreaves/kinto