It's a good topic. I often think that an application built with PureMVC or any MVC framework could benefits a specific documentation design that explains how it work in a more comprehensive way.
I also first adopted PureMVC because of its clear and sufficient documentation. It's a big advantage in project management when project have to go from the hand of a developer (team) to another often in the life of the product. I think it's a good thing to continue the work Cliff has done while well documenting our own applications.
Do you use sequence diagrams or use cases to document commands?
In my project management, I document first with UML, I separate use cases and create the sequence diagram for each. It's more than often that a command exists for a specific use case. I think that it's a good practice to think it this way.
I'm an Agile adept, so I think in term of "the less documentation we have, the more Agile we can be when the project needs to be refactored or modified". It's why I think I will never use UML class diagrams to describe a project. But if you think you need it, the code can be easily reverse engineered using the appropriate tool (Entreprise Architect can reverse AS2,AS3). I prefer export an ASDoc with a rich inline documentation (javadoc comments) or to use the "View source" generated by Flex as here on PureMVC.org.
But to be honest, as you I want to find a way to better document the core design of my application with some drawing that tend to separate View, Model, Controller, WebService, LocalStorage etc... To represent in only one design a whole PureMVC core.