The main tradeoff for using EKS is the built-in CNI is limited by the number of virtual IPs you can assign to a given node type's network adapters. If you are running a bunch of small workloads you end up with very under-utilized compute and if you're using autoscaling that results in a lot of churn. We replaced it with weave-cni which has it's own set of headaches in regards to pod access to the control plane but it does allow us to run a basically unlimited number of small workloads on somewhat beefy instances. We set it up using spot pricing and the costs have been very low.