I don't use Gnome so it doesn't matter to me but...

> Having two completely separate mechanisms for copy-paste (not talking about the UI, but the underlying clipboard/selection) genuinely is confusing. It's never consistent across applications. Will I be able to middle-click paste from this web browser to that terminal, or from this emacs to that Skype window? Or do I need to select + Ctrl-Insert in this terminal to copy to that other window.

In my experience, middle click is an X thing and is the only thing generally guaranteed to work practically everywhere.

For this reason, it seems not justifiable to me.