One of the cool things about software based recorders is that we can break away from established paradigms in the hardware world.  Since tracks and busses can be created on the fly in the software world we have the potential to re-think their role in the mixing process.

Personally, I'd like to see a top-level folder that is the "master bus output" and then sub-folders under that which represent the busses that feed the master, and so on.  The lowest level would represent the actual tracks themselves.  This way you could easily view your project from the highest level and drill down as far as you wish to go.  

I know the idea of using folders as busses has been suggested before (I believe that Rasure's link above does so too), but I can see why there might be some resistance by those who'd prefer to keep the dividing line between tracks and busses either because they are used to this paradigm from the hardware world, or simply because it makes more sense.

The great thing about software though is that it should be possible to support both approaches, and I bet we can do so without adding a lot of complexity and bloat.  It really is more of an organizational way of approaching the same thing:  audio data being routed from one place to another.