Yeah, I like the system Grendel mentions it's close to most CAD packages assembly tree layout, but then I like PaQ's idea about the quick access on/off/hide system. 
So that last graphic you have there Grendel is the best of both worlds, which is cool, but, the size of that tree is a bit big, I thought anyway.
 
So I stared at MoI for a while and had this in mind, so I thought I'd throw it out here for discussion. 
It was quick so I might of missed something.
 
It functions like the OSnap except it has 3 clicks for the tick, which are ✓ for normal operation X for Non Selectable and blank for hide and the rest is self explanatory.
  
~Danny~  
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