Nix already solved the first problem a while ago, though its adoption is hindered by the fact that it would essentially deprecate the entire infrastructure that actually makes a distribution a distribution, and is therefore unaligned with best interests. This is in spite of widespread claims of wanting standardization.
Nix is just simply amazing, and there IS a distribution (NixOS[1]) which ships it. The big problem is of course keeping packages current.
Nix and SmartOS[2] are both really important in my book. Nobody's talking about them as distributions but they both have intense potential to completely change not just server-administration (which is what they solve right now) but having a nice desktop experience. It would look like the Windows desktop experience, where they try to hide C: from you and just give you a set of shared-across-your-applications folders: Documents, Desktop Icons, Pictures. When every application occupies its own universe, then the OS itself behaves just the way that the "window" metaphor suggests; moreover you can start to seamlessly include VMs and get Windows applications living next to OSX ones. The only cost is hard-drive space, but hard drive space can be shared if we can package the software and share packages with the same checksums.
Eventually, I hope that people will just assume that an application "comes with" its operating environment.
