My experience is that iTunes can't handle anything but perfectly neat metadata about album versions of songs. Every time I've fed it live music, or alternate takes, or anything else weird, it's choked so badly that I ended up wishing for no organization.
Agreed, for a lot of people "no organization" is a feature unto itself. iTunes is famous for mangling already cleanly-organized collections of folders on disk, etc.
http://beets.io
It's more powerful than iTunes and can sync with databases like Discogs and Musicbrainz to keep data up to date.