Surely you can have one layer per directory or something like that? Splitting along those lines works as long as everything isn't in one big file.

I think it was a mistake to make layers as a storage model visible in to the end user. This should just have been an internal implementation detail, perhaps similar to how Git handles delta compression and makes it independent of branching structure. We also should have delta pushes and pulls, using global caches (for public content), and the ability to start containers while their image is still in transfer.