Sometimes you want a single filesystem, sometimes you want multiple filesystems, sometimes you want an image copied into RAM and nothing more, sometimes you don't have the resources to even load something like FUSE.
I believe that if we are to make anything better we have to be able to either switch or combine the many ways one can make a modular or composable system.
We can already swap bootloaders, kernels, desktop environments, transplant storage from one system to another and continue working. It should be just a feasible to switch filesystem/package models.