I have been an AutoCAD user for more than 15 years. I always thought layers is the only way. Then, I bought Revit and I was amazed to see that grouping and categorising is easier. After that, I saw MAX where naming and handling the list of objects has many advantages too. Layers are a well tested system, it works but there are others too.
Also, the power of modifiers, the history tracking and changing and the properties dialog are some of the greatest benefits of today's 3d modeling apps.
If MOI can use and adopt this logic it will be a best seller.

AutoCAD is so general that everyone and nobody needs it 100%. The same with MAX. MoI (so far) has very effective tools, not 1500 commands like most of the apps do. I guess many other commands will be added but I believe that the menu system and the navigation buttons make our life easier.

So, I guess Michael will have to come with some difficult decisions on how to combine all these ways of handling objects.

In my opinion, the new release of Cinema4d (r.10) is a also a very good exemple for scene management.
It combines a layer system with a scene / hierarchy tree so you can use either or a combination of both to keep things organised