I PoCed EKS for our company. Significant issues we experienced vs Fargate were that EKS had no sane logging story out of the box--you had to build it yourself.

I PoCed EKS for our company. Significant issues we experienced vs Fargate were that EKS had no sane logging story out of the box--you had to build it yourself. Worse, EKS didn't integrate with IAM and we couldn't figure out a sane workaround. These issues are more-or-less addressed on the containers roadmap, so things are improving, but there's good reason to use Fargate. Also, I can't imagine feeling "locked in" to Fargate; porting to Kubernetes is pretty straightforward unless you depend on some isolation property provided by Fargate.