When VMs take tens of seconds to boot, Hyper is able to launch instances in sub-second. Also, Hyper requires the slimmed resource footprint: 28MB RAM, which means higher density: run hundreds of Hyper instances on a server, where a dozens of VMs would overload.
Hyper is immune from the "shared kernel" problem in container, because virtualization offers an excellent Hardware-enforced Isolation. The attack surface for a VM instance is quite small, as it lacks the variety of functions (and, therefore, the potential flaws to be exploited) provided by standard operating systems.
Hyper is hypervisor agnostic. The current implementation supports KVM, Xen, and VirtualBox (according to the platform), with more in the roadmap. Combined with the portability of App Container Image, Hyper allows you to build, ship, run app anywhere, without worrying the infrastructure technology stack.
Hyper eliminates the need of Guest OS. There is no moving parts inside of a Hyper instance to be configured or managed. The entire stack is Immutable.
In a multi-tenant environment, the platform must allow developers to pick different kernel and modules. This is an easy job in Hyper, but very hard to do in containers, due to the fact of "sharing the host's kernel".
Virtualization is mature. Features like LiveMigration, SDN, SDS have been battle-tested for years. With Hyper, you can just Plug & Play. No need to wait another two years for the container-version SDN.
Virtualization is widely implemented among enterprises. Instead of rebuilding everything with containers, Hyper provides a Seamless Migration path to your existing virtual infrastructure.
The following table gives a more detailed comparision between Container, (traditional) VM and Hyper:
Weak, shared kernel
No, hypervisor dependent
Yes, hypervisor agnostic and portable image
Slow, tens of seconds
Good, minimal resource footprint and overhead
No, configuration management required
Yes, guest os is gone
No, brand new world
Great, everything still works
Good, still a "Machine", much less changes
Yes, production ready, SDN, SDS, LiveMigration, etc.
Yes, just plug-&-play
Low, rebuild everything with container
High, seamless integration with your virtual infrastructure