Problem: I have very large files with thousands of layers. I organize them into screens, dozens, sometimes hundreds. Because you can only prototype root level frames, I have a ton of items at the root level. (100+) This makes it too hard to find things.
I really want to organize those and keep it working with prototypes. Pages is unacceptable because you can’t link between them, but also because it separates things TOO much. Even if I had 1 level of grouping at the root it would dramatically reduce the number of items on the left and make it much easier to find things.
Solution: Since frames, pages, and groups all have important meaning, I would suggest a new object called a folder that allowed you organize things, but did not have any meaning other than that. No shadows, strokes, etc.
It could work only at the root level if that made it easier to produce.