A Whonix Host Operating System has been a long standing TODO item that hasn’t made much progress over the years. Providing more usable user interface than VirtualBox, the ability to easily fire up additional VMs, to open potentially dangerous files in a disposable VM, easier file transfer in and out VMs, backups, host firewall and so forth. Not to mention hardware driver support Whonix would have to offer. While the Whonix project has insufficient funding as well as contributor manpower to realize any of that anytime soon, fortunately there is the Qubes OS Project. A Xen / Linux based distribution that focuses heavily on security compartmentalization. That means, for example, network devices are running in their own virtual machine. Any vulnerability in the network stack or card would be contained in that virtual machine. Firewall runs in another virtual machine. So does an untrusted browser. Everything can be compartmentalized into domains. An exploit inside an untrusted domain is contained and cannot compromise a private or work domain as long as the adversary cannot compromise Xen as well. Fortunately, Xen has a smaller attack surface than Linux. You can read more about Qubes architecture on the Qubes website. Furthermore Qubes implemented all of that while providing user interface with good usability.
Over the last few months Qubes-Whonix, a port of Whonix to Qubes has been developed. There has been a lot interest in this. And there is more to do.
After the release of Whonix 11, which is a port from Debian wheezy, sysvinit based Whonix to Debian jessie, systemd based Whonix [and more], my personal focus will shift more and more towards development of Qubes-Whonix.
For now, physical isolation (“–target root”) is not planned to be deprecated, because the Qubes-Whonix build process uses something similar to “–target root”. Neither the VirtualBox builds of Whonix are planned to be deprecated. Those are still a good way for new users to get in touch with Whonix and Linux in general.