If you want a nice-from-first-principals approach to package management for desktop apps, Flatpak is the shit: it uses a Git-like distribution system that's specifically built for operating system size snapshots. You get to pick your underlying distribution (or roll your own) and the sandboxing mechanism just wraps around secomp-bfp so it stacks well with SELinux or AppArmor or whatever.
But now we are going to have yet-another-bifurcation of OSS solutions: RPM vs DEB, KDE vs GNOME, Wayland vs Mir.
Canonical, stop trying to be Apple, please.