I think the ayatana mailing list is better suited for this kind of discussion. 
Just this:
@JC, @Michael
Both suggestions are too complicated, also middle click is already occupied for 
launching a new instance/window. What about minimizing the whole app (all its 
windows) from the context menu and a minimize button per window in the scale 
view (together with a dedicated close button, there should be a bug for that 
too)? The scale view could further be improved, a possible implementation here: 
https://lists.launchpad.net/ayatana/msg05651.html

One thing is certain, the old taskbar window minimizing behavior is not
coming back unless the whole taskbar makes it back into Unity. An
application dock simply doesn't work that way, like it or not. Though
there are several standalone taskbars available you could use together
with Unity (for example tint2, probably gnome-panel too if someone
patched it).

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https://bugs.launchpad.net/bugs/733349

Title:
  Minimize windows upon clicking application's launcher

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