Having been running a large scale production system on ECS for well over a year now, I'd like to say that ECS is hardly a bad choice; it's incredibly stable, integrates with proven AWS technologies (CloudFormation, ELB, etc) and it just works without having to manage clustering. All it needs is a layer of usability on top, which you can get from things like Empire and Convox.

While native Docker clustering is cool in theory, I think the vast amount of complexity around networking makes it unsuitable for production deployments at this time. If stability is more important than bells and whistles, ECS is great choice. Docker's production story, outside of simply running containers, has a lot to be desired.