Just thought I'd throw out an idea for scene management(really looking forward to that). The idea is to have the standard interface you have now with the scene tree pane hidden. You click the Scene Tree button on bottom right of viewport and then it expands from the right toolbar. So this way if you have a simple scene and don't need management it does not add clutter other than one icon at the bottom right. It is scrollable(is that a word ;)) for big assemblies on the right of the panel. The square opens a color selector pop-up to change the items color. The circle would be a visibility button to toggle visibility. The tree would be a drag and drop nesting approach that is collapsible with the + boxes. Their is also another unused tab at the top of the panel( A nifty little ambient occlusion render or an HDRI preview render would be great but I know that is a ways off)