There's several things going on here with duplicate music, I see at least these cases:
1) Identical files with identical names
2) Identical music but different quality
3) Identical music but different format (m4a and mp3)
4) Identical music, same quality and encoding but the files differ
Ideally I'd like something that solved all of these problems without a lot of work. Let me propose a solution and maybe this could be a plugin or perhaps a mod to MusicBrainz:
First and easiest, 'Overwrite' option that instead of creating (1), (2)... versions. Minimally you could ask like windows does 'What do you want me to do, overwrite, create new name, do this for all the rest?'
Second, when the two formats are identical and it's only the bitrate that is different, there could be a check box to prefer greatest or least bitrate. This may not actually translate to best fidelity but that could be much harder and this is probably good enough 90% of the time!
Third, when there are multiple formats, you could simply have a list in the options which order to prefer when overwriting. Again, you could ask this in a popup (which to keep? The .m4a or mp3 or both?) And this would be triggered if the Overwrite option was selected.
On using an acoustic fingerprint, I don't now if Picard does this or not but it does seem to find a large percentage of the music correctly.