Hmm, that sounds like a possibility, though as a practical matter every UI application I can remember using on Linux uses Ctrl-C / Ctrl-V, and terminal applications use Ctrl-Shift-C / Ctrl-Shift-V - because Ctrl is for sending signals to applications (like Ctrl-C). That's universal enough that I don't see any issue. (Actually I prefer it to the way Apple separates Cmd and Ctrl, which I find infuriating because of the awkward finger positioning it requires.)

Ctrl-Y, a la emacs. E.g. Matlab uses that by default.