What is the best way to arrange prefabs in the hierarchy?

I hope my prefabs are managed well and I wonder about the difference between saving a prefab with many child objects, when each child is a game object of it’s own, or saving one game object and duplicating it. This is how it is in my scene right now:
99988-all-object-is-a-prefab.jpg One object as a prefab
99989-the-whole-group-is-a-prefab.jpg many objects grouped together and made a prefab. In the scene the player can pick each object individually.


One major problem with prefabs still is that they don’t support nested structures. This means, whenever you save a prefab with it’s children, being a gameobject or a prefab already, this information is lost and the new prefab will hold all the information. Managing what you think is still a “sub-prefab” is not the case anymore, it’s one bigger prefab.
It depends on you needs. Think what needs to stay individal and keep it a seperate prefab. Otherwise, one revert can ruin your uniquely setup gigantic prefab.
Hence, there’s no best way of arranging prefabs in the scene. I’ve heard of a team that prefabed plain everything, which I think is a very bad idea.