Thanx to Juan Carlos Franco, there's finally a binary version of my Prefs:ImageConverter tool which allows you to specify custom video/audio data rates, frames per second and resolution for your MP4 files. The tool is ever so simple and ever so powerfull:
Just download either the binary ZIP or the binary EXE from http://hansschmucker.free.fr/clie/Prefs-ImageConverter/
and start it:
Now just select the profile you want to alter, adjust the settings and press Apply. You don't even have to restart ImageConverter. Just add a new file, select output to MS and your profile and you're ready to go!