Out of curiosity, do you keep 1-1 mapping among users/groups/roles(/resources?) across different accounts? Because that's another possible source of complexity.
For IAM Roles, we use Infrastructure-as-Code (Terraform) to create all those anyway, so I still prefer to create those in the AWS account that contains the resources to which they apply.
[1] https://aws.amazon.com/blogs/security/enable-a-new-feature-i...
I'd be interested to see your team's workflow for multiple accounts @joshpadnick.