You rely on a couple of flawed assumptions. First; it is not obvious that Mark Shuttleworth makes all these decisions. I hardly believe Ubuntu would've become such a success if he was a one-man show. It is a collective effort. Also, you assume that "this really handy function" has been thrown away. It hasn't.
Ok, now let's look at your question. It seems to be about how to launch a new instance of Firefox when there's already one running. Easy; middle-click it. Or if you use keyboard shortcuts, append Shift. For instance, if Firefox is number two on your launcher, press Super+Shift+2 to launch a new instance. You can then use Super+BAT (button above tab) to switch between Firefox instances, and you'll be moved to the correct desktop if they're on different ones. It will remember the window order, so you will also be able to use Alt+Tab to switch between the most recently used instances per application.
The cube and other Compiz effects are still available. Unity itself is a Compiz plugin, so none of those options have been removed.