Well, the comfortable thing with using multiple SWFs is having the instance of the plugin ready to work with as soon as the SWF finishes loading.
What might work without any actual engine changes, though, would be to write a "compound" plugin, which just forwards all calls (register, initialize,
attribute handling and so on) to a fixed list of plugins that are compiled into that compound plugin... might try that out some time, to see how much
filesize that saves.