The main problem is that there are decades of software developed for the classical filesystem, and Nix proposes just to patch that software so that it would be

The main problem is that there are decades of software developed for the classical filesystem, and Nix proposes just to patch that software so that it would be compatible with the "new" way. This is a radical and unneeded change. It would be better to just run software in separate namespaces and just provide whatever filesystem it wants, instead of forcing your own true way.