Flynn is designed to be an end-to-end solution for production deployment, and all of our components are created to work together. The whole system is self-bootstrapping and self-hosting, so installation is easy, and the same APIs are used to manage the whole platform as are used to manage apps deployed on it.
In addition to the twelve-factor stateless webapps that Deis Workflow supports, Flynn also includes highly available database appliances with safe, automatic failover (currently PostgreSQL, MySQL, and MongoDB with more coming in the future). We also have a bunch of security features coming over the next few months like Let's Encrypt support and flexible user authentication with 2FA and very granular access control.
If you don't need or want our database appliances and you are comfortable with Kubernetes and happy to install and operate it, then Deis Workflow is a good option. If you don't care about using Kubernetes specifically, Flynn is a good pick as it is easier to get up and running with.