From a developer perspective, any new project we will be working on, unless specifically requested by the client, will be on top of Kubernetes. Actually, Kubernetes compete with Marathon as a container orchestration software, and as far as I know, one could run Kubernetes over Mesos. So, assuming your PaaS will serve developers, I would take a closer look at Kubernetes first. The goal for Mesos project is to be a sort of kernel for distributed computing, while Kubernetes is to manage the deploy and load balacing o of containers. Either way, you will need a container orchestration solution and the one to go with, given the current tendency in the market and the ecosystem around it, is Kubernetes.