Like I think all of the Systemd stories, sensational article is sensational. If you actually read what machinectl is, you'll see it has nothing to do with the su command, and it's also not suppose to replace it. Basically, from reading for about 1 minute, machinectl is to execute operations on VMs and containers. Last time I checked, the su command don't do that and have nothing to do with it. Probably someone asked Poettering, "Hey, would be nice to have root shells in a VM"
machinectl may be used to execute operations on machines and images. Machines in this sense are considered running instances of:
Virtual Machines (VMs) that virtualize hardware to run full operating system (OS) instances (including their kernels) in a virtualized environment on top of the host OS.
Containers that share the hardware and OS kernel with the host OS, in order to run OS userspace instances on top the host OS.
The host system itself