I think the biggest difference is that Flynn is building a scheduler modeled after Google's Omega paper (what they call Layer-0) along with the Heroku-style platform components (which they call Layer-1) -- all written from scratch in Go.

Deis, on the other hand, is laser focused on the platform problem. We're also not shy about using off-the-shelf components where they make sense. For example, we believe the distributed scheduler/init system is best left to others like CoreOS/Fleet.

gabrtv is correct that Flynn is built on a scheduling framework (think Mesos, but based on the Omega paper), which allows us to support running stateful services (like databases) inside of the platform.

Flynn develops most core technologies internally. We try to minimize our external dependencies, as the majority of instability we've run into has historically come from dependencies.

Building modular, reusable, and repurposable components is also a major design goal of ours (for example, Deis uses a few Flynn components).