My biggest inconsistency with Cloud Formation is with smaller AWS offerings. If I need to build a VPC with some EC2 capacity it works well. If I want to create a load balancer and use R53 to do DNS based certificate validation with their in house SSL provider, I'm out of luck.

It looks like internal products need to work with cloud formation to enable support, and aws doesn't have a consistent model here. It seems that they are fine with some products cutting corners and not offering support (like DNS based certificate validation)

Inconsistency within aws isn't all that surprising.