Wouldn't it be great when Compositions with massive numbers of Layers could be organised in Layer Folders (a bit like Photoshop can do).
These Folders are different from PreComps:
1-the folders are foldable/unfoldable to give access at any moment, without leaving the Composition
2-the Layers withing the Folders act like normal Layers, and can have different compositing modes to influence all Layers underneath.
3-Layers inside and outside the Folder can refer to eachother (Set Matte, Parenting, Expressions, ...)