I have considered using other 3rd party tool, but found that all the tools that might have been relevant are no longer available. I was left with a choice between using Director, with its unsatisfactory alpha-channel support, or Flash with it's problematic FLV playback control. I had eventually decided to use Flash and to embed the FLVs in the Flash timeline. I've found out that Flash, especially (but not exclusively) because of the embedded videos, could not cope with the great number of calculations required, and the playback was sluggish and buggy.
A lot more on this subject
A lot more on this subject