Perhaps core Moodle needs dedicated multimedia plugins? i.e. something that can upload and deploy all the required files for HTML5 and Flash based multimedia activities/presentations.
At the moment, the easiest way to deploy multimedia in Moodle 2.x is to embed it all in a .swf file (like many SCORM authoring packages) and deploy that as a resource (no interaction with Moodle's back end though).
If Moodle HQ are really serious about providing alternatives to Flash, providing adequate support for HTML5 multimedia should be a priority. Meanwhile Flash has been made a priority open source project by Apache (ASF): http://flex.apache.org/ (the Flex SDK has always been open source) and you can develop Flash apps in an excellent open source (Netbeans-like) IDE now too: http://www.flashdevelop.org/ Funny how what goes around, comes around, eh?