I wonder what the chances are Canonical's already planning to put file navigation into Unity. It could look something like this though;

The bar down the side lends itself to integrating file system navigation, because you could have seperate Unity layers spring out whenever you moused over a folder. Seems logical?

In an ASCII world it would look kind of

Code:
-----------------------------
|X                            
|o                          
|o                          
|o                          
|o                          
|o                          
|o                          
|o                          
|o                          
-----------------------------
If you click or *mouse over* the Ubuntu button you get the familiar text search for applications, music etc. Full or partial screen.
Code:
-----------------------------
|X [___________]           
|o o_o_o_o_o_o_o           
|o o_o_o_o_o_o_o            
|o o_o_o_o_o_o_o            
|o                            
|o                            
|o                            
|o                            
|o                           
-----------------------------
Mousing over a folder pops out another vertical Unity column, but this one's a vertical Nautilus, which also swipes up and down like first column does when it's full.

Code:
-----------------------------
|X +                        
|o o                        
|o o                        
|+ o                       
|o o                        
|o o                        
|o o                        
|o o                        
|o +                       
-----------------------------
Applications and data files are static unless you click on them, but file folders or shortcuts, which may still be placed arbitrarily as in the first column of the launcher, fly out.
Code:
-----------------------------
|X + +                        
|o o                        
|o o                        
|+ o                         
|o o o                        
|o + o                        
|o o o                        
|o o                          
|o + +                         
-----------------------------
You'd keep nautilus for when you clicked folders.

You could just use shortcuts to recreate Gnome-2 type Application Categories this way as well. Might look nifty on a touch-tablet phone too ;^,