- severe unchangeable, undocumented limits before you get throttled. Throttling is so bad that if you have too many parameter store resources in your CloudFormation template it will start causing errors because CF is trying to call the API too quickly - the only way around it is to use DependsOn and chain the creation.
- no way of creating an encrypted value with CF without a custom resource.
We ended up just using DynamoDB for config anda Custom CloudFormation resource to create values in it.
You should never depend on Parameter Store as a reliable key/value store for configuration.