This is probably a question better suited for the Compression Techniques forum.
A question that might make a difference…
1) Who is Target audience?
> high end user where quality is everything and their connection is fast.
to
>phone modem user where getting the 3min message is important and a reasonably small file for download is paramount.
Often I will encode and embed Flash and will have a downloadable WMV available for slower connections.
You may want to include the Flip4Mac product to encode WMV from QTPro.
Not a complete answer but hopefully a start in the right direction.
Cheers,
Joe
L.O.A.