Comment 209 for bug 733349

As Ubuntu Design Team says - it's only to make the desktop feel consistent. They're worried about what should happen when user clicks on icon which has two windows. This won't minimize and will make users feel confused.

But, I simply can't understand HOW this will confuse users. Unity should allow minimizing ONLY when there's ONE window underneath the icon; simply - do something instead of doing absolutely nothing. When there are two windows, Unity currently shows spread and that's perfect. This is simply reducing usability a lot. Hope the developers will notice that.