OK, this is what I think so far...I will try to find the best way by analysing the way three apps work... AutoCAD, Revit, Max. This is the only experience I have from 3d apps.
Layers are very easy, very fast and very flexible since you can change an object's layer whenever you want. AutoCAD for example, needs layers because it is a general drafting application so there are no categories by default... You can draw what ever you want and the layer shows where the object belongs to... The grouping method was always blocks...AutoCAD objects where always "dead" objects... You want to change something, you have to do all the work again, no connection between them and there was no way to update the changes in real time... For example when I move a wall to a floor plan, the section will not be updated, I have to move the wall there too.
Revit has no layers at all... Because it is fully oriented application there was no need of them... We have categories, names, group names...styles... things that can help identifying all objects... For example we have a "Brick wall 20cm" from level 1 to level 2, and level1 has a distance of 3 meters from level2, so the wall is too 3m high, and it has a door and a window that can't exist without the wall... Everything is connected, I move the window and I have all sections and elevations updated in real time.Revit has objects so layers are not needed.
Max, has layers to be compatible with other Autodesk products. When we start a scene in max, we have objects that get a name by default but can easily be renamed by the user. We have a list of objects and we can pick by name, by material, by layer... Also we can group objects so that they behave as one (moved together for example) and also create named sets so that the objects are not connected like groups but they can be selected together.

I think that the system Michael should choose for MoI depends on what kind of features will be added. For example, if we have object modifiers and modification history, layers don't work... We got to have named objects. Also, if curves and solids are connected (as they should in my opinion) we need some hierarchy tree like Max's modifier stack.
Since sub object handling (vertex, edge, surface) will be added the hierarchy tree will be important.