@Psyko, I figured out the ideal solution. This was annoying me as well, so I thought I'd register and share!
Simplest hack is to
move all files you want excluded
to a File Sharing folder (like VLC). If you really want to keep that 740MB VLC data backed up, though, use another app like Chrome. These file sharing folders are located in
On My iPhone.
If the folder is not there, copy at least one file into File Sharing (with iTunes on Mac or PC), then the folder will be created in On My iPhone on your device. Stash the files in that folder, then exclude the app from your next backup.
Below is my screenshot showing VLC excluded. Hope this helps!