Converting WMV files to QuickTime  and file size

I have QT Pro and I have no problem doing a "save as..." for converting WMV files to .mov. I also have Flip4Mac converting the file to be viewed in QT first.
My question is that if I do a straight-ahead "save as..." it'll make the file's size about 25% larger. If I try to do "export" with default settings it takes far longer and I have an even larger file. I've also tried playing with different compression in QT to save these files and haven't come up with anything that works better. Is there a way to manage the file size so it's the same or smaller, not bigger?
Thanks in advance all!

File size is dicated by the bitrate of the file. From my review of (thousands) of WMV files there appears to be some compression in the WMV format that is not reapplied when save as to a MOV container is performed. You can see in get info the WMV file say 100MB has maybe 125-150MB of data when it is fully loaded in Quicktime.
Thus save as does not apply the WMV compression the same as native WMV is all I can assume and the new QT file (MOV container) is bigger than the source file is.
Exporting to any new QT format (say H264) is going to make a file that is dependent on the new QT bitrate you select but if it is higher than the bitrate shown in the Get Info Inspector box when the original WMV has been opened it will be bigger without a doubt. So if you have a 3Mb/sec WMV file that you export to 700 kb/sec for iPod basic it should be 1/4 of the size. Use 5Mb/sec fo Apple TV it should be 2/3 larger.
I rarely use QT Pro to export and when I do I don't use default settings. I prefer MPEG Streamclip which offers easier control of variables, batch file processing, deinterlacing and other things and it is free.

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