For some reason, Unity has made it a chore to work with their scene graph.
There are loads of problems with it: there's no root so you can't actually traverse the whole scene without using tags, there is a terrible traversal API (IEnumerator or GetChild(int)), you can't add and remove objects from the scene graph, in code it's difficult to tell whether or not a GameObject is a prefab or an instance, there's no central management of the scene, the Transform-GameObject relationship is simply weird as there is a 1-1 relationship but only one of them allows graph traversals-- the list goes on and on.
Why couldn't they have a simple SceneManager that makes everything a bit simpler? The Unity scene is literally the same as an XML document-- we could use XPath, e4x, or like that link I just shared, some other mashup of the two.
You don't even need a manager, you could slap it all on the graph node: Transform. All you'd need to manage the scene is a single root node and you could fly!
WE KNOW SO MANY THINGS ABOUT GRAPHS.
Yes yes, I know what you're thinking: you could just organize your scene such that there's a root node and you could just write a bunch of extension methods. This is true, but you're going to be fighting it forever. If you do new GameObject(), guess what, it's not going to be a child of your root-- and extension methods can only go so far.
I am constantly reminded of how terrible Unity is at this. Just this morning I was forced to write this:
public static void Walk<T>(this GameObject @this, Action action) where T : Component; ... myGameObject.Walk<Renderer>(renderer => renderer.enabled = false);
Which, while cool, reminds me of exactly how much better Unity could be.