Hey Mitch - great question! I have been testing the extent of this as I needed more interactivity that I can normally get via scripting, so using the commands is a great way to go, I think. Still trying to figure out its limitations and possibilities. I have started a topic with some questions, observations and expamples:
http://discourse.mcneel.com/t/running-scripts-inside-rhino-commands--runscript-vs-compiled-plugins/26341