The PluginManager uses two MediaFactory objects, but the second one is an implementation detail. (The implementation uses a MediaFactory internally to do the plugin loading, but that never surfaces to the client.) Any time you load a plugin via the PluginManager API, the loaded MediaInfos should show up so that calls to createMediaElement do return the MediaElement from the loaded plugin. If you're not seeing this behavior, let us know.
It's possible I am doing something wrong, but here is the gist:
Create a media factory
Create a pluginmanager, passing the mediafactory to its constructor.
Create a new pluginInfoResource( passing it a new instance of a PluginInfo extension of mine
Inside of the constructor of that plugin info, I create an array of media infos and pass them upstream through the constructor
Later I call the createMediaElement method of the mediaFactory mentioned above and pass it a resource.
It fails, and if I debug it, the infos inside of the MediaFactory is empty.
ah, nevermind. it is because I had the MediaInfoType of Proxy set on the MediaInfo of the Plugin.