Hi Don,
Re: multimedia in general, I think there's a danger of ending up with a situation where organisations who are looking for an LMS as a platform for multimedia consider Moodle unsuitable and look to other LMS' and so those who do use Moodle and would like better support for multimedia a fewer and therefore have a smaller voice. Then Moodle HQ can interpret that as multimedia support is of insufficient demand or interest.
Moodle 2.x already excludes uploading sequence multimedia into the files directory API. It's a real headache if you want to deploy Flash, Java, or HTML5 sequenced media, e.g. https://moodle.org/mod/forum/discuss.php?d=207612 It has little to do with whether a sequence requires plugins or not -- Plugins like Flash, Java, Quicktime, etc. are not the issue. In each case, it looks like someone needs to develop a new Moodle plugin or use an external 3rd party file repository to deploy multiple multimedia files, something that other LMS' and CMS' have no problems with.
Re: plugins and filters, look at how the basic media filters work: They indiscriminately filter every URL that's posted sitewide. They're either on or off. It's like having a car with two speed controls -- Stop & Full speed... or perhaps that's how they drive in Perth, I don't know :P
Can't we learn from other media filter implementations in other software? Perhaps reach for something a little more subtle, controllable, user friendly, and useful?