Please also think of using "named sets". Also, an automatic and editable object naming is a must to organize our objects... MoI will be used for complex product modeling where small parts will not always be easily selected so using names initially given by MoI and edited by us, will be an easy way.
Layers can be used as a second grouping method.
For example... All metal parts will be on layer "metal", all plastic parts will be on layer "plastic" but a handle can be plastic with metal bolts so a group named "handle" will contain parts from both layers and can be exported to a file, improved and re-imported (maybe at the same place).
I like this scenario very much and I find it very useful.
Just a thought...