After upgrading GCE cluster to 1.5.2 I need to customise kube-dns configuration. I can save my changes to kube-dns deployment, but they are being reverted back to default after some time. I tried removing kubernetes.io/cluster-service: "true" labels with similar outcome — it reappears again after some time.
Kubernetes 1.5 comes with a new system service called kube-dns-autoscaler (documentation) that automatically adjusts the number of DNS replicas in your system based on the number of nodes and cores that your cluster has.
You can tune the autoscaling parameters to indirectly adjust the number of DNS replicas rather than trying to adjust the number of replicas by modifying the kube-dns deployment directly.