cddb style scripted solution?
The current alias-file solution seems most apt for your problem, it's just not easy enough to be practical.
Why not set up some sort of foundry database that would regognize fonts by set properties in the ttf format (or others) and respond with the alias lines needed to fully organize one's collection? Sure a new font format that does everything everyone needs would be wonderful but don't expect to see it any time soon - and I think the database would make an acceptible and adaptbible solution.
Making alias files is already scripted locally - how difficult would it be to get some more advanced font-recognition into said script?