Overall question for going from a Flash file to MP4

Hey everyone.  I just have a generic question, especially for Flash users.  How would you advise someone who is using CS4 to get their video file to an MP4?  I've tried Adobe Encoder and iMovie and the MP4s are still bigger than the original swfs.  I had been exporting my Flash files to .mov files and then taking those .mov files and making them into MP4s.  I'm wondering if the .movs are so big that I can't make the MP4s smaller than the swfs, but I can't compress the .mov files or the video looks horrible.

So, maybe my whole process is wrong.  Starting from the beginning, how would you users recommend making a Flash file into a MP4?  Any help, suggestions, and person experiences would be GREATLY appreciated.  Thank you so much!!