Yes, I think it would be great to be able to create the key otuside of the physical hardware token, just like you can do with the GPG applet on the Yubkey. Store the original on some offline, encrypted media, ideally in multiple places.

This way, you don't need to have two yubikeys on hand and register them both on every new site. But in case you lose, it's not impossible to create a new one. Yet, obtaining the key from the hardware token shouldn't be any more possible than with the current system.