We are currently looking into creating more development tools for widget-creation. Right now we only have the brackets plugin, but this should be more generic. More plugins for other editors and IDE's, or scaffolding tools like a Yeoman-generator.
I think it would make sense if instead of just dropping in a .zip (sorry, .mpk) in the widgets folder, you would also be allowed to have a directory with the widget files there. When building the application, Mendix would pick this up (I bevlieve it will extract the .mpk to the deployment dir anyway).
Same goes for theme files.