My next project will use Unity 5.6. It will be a game and that will leverage AssetBundle for remote scenes loading. New scenes will be incrementally added afterward. Therefor
Unity actually does encourage the following structure:
Assets
├── Animations
│ └── ...
├── Editor
│ └── ...
├── Models
│ └── ...
├── Prefabs
│ └── ...
├── Scripts
│ └── ...
└── Textures
└── ...
This is due to the object oriented way in which Unity thinks: Each folder contains only the information of a certain type needed for an asset. This is especially visible when you look at the Special Folders in Unity.
Even when you look at how they build up their standard assets you will notice this structure. I hope you won't have a lot of scenes which do not share any assets with the other scenes, because this would be a very big waste of resources.
What is notable in the Standard Assets, is that in their demo, they have a folder called Menu
which contains its own Scripts, Prefabs and Sprites folders.
So I suggest you do the following (note: This is my opinion):