On the other hand, I find it troubling that Quicktime takes over handling of swf files, since it's takeover of .wav and .au files is a real pain in the butt, if you're trying to use javascript to control sounds.
Unless Apple has enabled LiveConnect in the 4.0 plugin, which I bet they haven't, I really wish that QT would drop off if the user already had a plugin that handled a media type.
It will be much more troubling if now SWF files are not able to send commands to the browser, after all.