Maybe have a wizard that asks whether you are a completist / album collector versus a song collector. It took me a while to figure this out and to learn that this change required a restart of the scan.
My goals were to keep all FLACs in favor of MP3/MP4/OGG and to keep the albums intact. It kept marking FLAC files for deletion, so I had to rethink the scanning strategy. It would be nice to have a set of questions that would configure it right from the get go.