The main advantage against shipyard is that you only need to deploy one container to run Portainer, it's really simple and quick. Shipyard deployment is more complex.
Have you ever thought about adding support for kvm/QEMU/virsh-based virtual machines as well?
I've been looking for a easy to use interface that gives a comprehensive overview of virtual machines as well as containers as I'm often using a mix of both.
Cockpit [1] too, although that might be a bit more focused on single machine management than on clusters (don't use any of those - so I can't tell for sure)
The main advantage against shipyard is that you only need to deploy one container to run Portainer, it's really simple and quick. Shipyard deployment is more complex.