I would also vote for something similar to C4d's new release (r10).
It combines as mentioned already a scene tree, which allows you to parent objects, organize your scene etc....
Attributes ( such as visibility) are inherited from the parent, unless specifically defined for an object).
You can also define any object to serve as the root for the diplayed tree, which allows you to easily navigate through complex scenes.
This is combined with a search filer and selection filter system,
and with a layers system.

Quite good really in my opinion.
I have experience with Maya, 3dsmax, Acad, FormZ and Rhino other than Cinema4d, and I would say that I like the C4d system best.
MOI may not need something as elaborate as C4d, since it is only a modeler, and not an animation package.

What would be important to have as well is a good Isolate implementation, to work on just part of a scene.
And as mentioned already, a good way of importing / exporting file - organization structures ( be it layers or otherwise)