Imo stuff like Flatpak has the right idea - provide a rich but controllable set of features, API/ABI compatibility, while providing zero overhead isolation (same as docker since it relies on the same APIs).

I also rather like the idea of deploying programs rather than virtual machines.

Docker's cardinal sin imo is that it was designed as a monetizable SaaS product, and suffers from inner platform effect, reinventing stuff (package management, lifecycle management etc) that didn't need to be invented.