We evaluated ECS and Beanstalk but ended up writing a tool around building CoreOS/Fleet clusters (not currently opensource but I'm trying). We ran into similar

We evaluated ECS and Beanstalk but ended up writing a tool around building CoreOS/Fleet clusters (not currently opensource but I'm trying). We ran into similar complaints. CoreOS comes with Etcd which though initially unstable is now solid and incredibly handy for service discovery and configuration. We're using https://github.com/MonsantoCo/etcd-aws-cluster https://github.com/MonsantoCo/etcd-aws-cluster to configure it dynamically. We use etcd+confd to drive nginx containers for routing. All in all it works well. Our biggest problems are docker bug related and those we can generally handle by just terminating the node and letting autoscale heal the cluster.