So we shouldn't go with the obvious solution that will also take the least effort to teach people (pressing the key next to Ctrl instead of Ctrl) because a few people out there have already set those shortcuts to do something magical on their machines?

Why is that more obvious than simply adding the shift to all copy operations? Changing to use the windows/options key is a terrible idea.

Copy/paste would be the only operations to use the windows/options key inside of programs, so much for consistency! If we are talking about changing all keyboard shortcuts to use windows/option key instead of CTRL is even worse, you are suggesting we should suddenly change all shortcuts for everyone, because some people can't remember to press the shift in the terminal?

And then there's the fact that pretty much all window managers/desktops use the window/option key for window manipulation (which sort of makes sense). That's not a few people that is almost everyone using keyboard shortcuts of their desktop environment.

Ctrl isn't near Cmd on my keyboard. And wasn't traditionally, even on first apple computers it resided where modern caps lock (an absolute waste of space) is.

Your solution is obvious to you, because you don't want to acknowledge the needs of others.

Alt+C/V, if anything, should be a better compromise, IMO. But it's still a compromise, not an obvious solution.