Yeah, I noticed this too. I often used it to zoom in on pictures with small text (though that might be unnecessary on my new rMBP). I can't see any reason to get rid of it, or at the very least leave it as an option that you can turn on.
It is still there. I use it with my trackpad all the time. Don't know if there's a difference between the trackpad and the mouse but is definitely there.
OK, I've just solved the issue.
Turned off the iMac, changed my mouse for an Apple one (borrowed from my flatmate)
started the iMac again and the option is available.
Checked it and changed the mouse again.
There seems to be.
When I come into my Mac through androidVNC, and then disconnect, my Mac is left with zooming in just the focused app window.
Opening Accessibility prefs and toggling a zoom-checkbox or two resets behavior to the normal full-screen-zoom.
androidVNC is probably touching some preferences plist to get that zoom behavior, but I've yet to figure out which plist and which item.