It is true that Mesos works on a different level, but, most of all, the two level scheduling is just a different take at the problem of abstracting physical/virtual resources. In the end, both Mesos/Marathon and Kubernetes aim at the same goal: allow developers to stop thinking about servers.
Kubernetes' great advantages is the community (which is unbelievable) and the extensibility it proposes: Third Party Resource or Custom Resource Definition, pluggable webhooks in the API Server and a number of other things that are simply not there in Marathon or any competitor which allow companies to make Kubernetes work best for their use cases.