Containers seem to be heading more in the direction of VMs. Which would compartmentalize the services of a given application, but then you might need a separate container for a given app. I don't know if you can completely get away from the problem of shipping code to new environments without configuration/customization.

Containers and libOSes/unikernels are two opposite approaches to remove redundant "yo dawg" layers of virtualization. It's not clear to me that a hypervisor+libOS is simpler than a containerized kernel, and Linux seems better maintained than Xen.