One reason I am hesitant to go this route is because I don't want to hard-code Amazon's API's into my apps..
For my own purposes, I weighed that against the alternatives[1], and it seems like a fairly reasonable compromise[2]. That won't be the case for everyone, obviously.
[1] http://elasticcompute.io/2016/01/21/runtime-secrets-with-doc...
[2] I'm referring specifically to passing secrets (or other static values) into a container, since that seems to be what the author was talking about. For configuration requiring more complexity, of course other tools are probably more appropriate. In that case, it's outside the scope of what I would reasonably expect ECS to do.
I know it's not sexy for developers to take advice from sysadmins, but at the end of the day, it gets the job done reliably and elegantly.