while it is easier that auto-sync will only keep 1 copy of the song, no longer when you're not sure about which song you have copied over it'll only have 1 copy of the song in retrospective that should hve been the default behavior of manulaly mangement music anyway.. it is probably extremely rare for someone wanting the same song duplicated.
The problem is you can't easily delete songs... Since iOS 5 that let you to delete, every time i delete something on the iOS device, and do a sync later the songs/albums i deleted kept syncing back! really annoying Since there is no option like Apps does, it doesn't transfer over if you don't want to.
Also i can't sort in iTunes on my iPhone 4S device when Auto-sync, it somehow stuck on sorting on PlayCount (that was what is on before i changed to auto-sync) and i can't change it... of course that list is where i delete my music manually and 100x better than the checkerbox interface which is extremely slow.
All that compromise with positive points like Playlist management which is much much easier... But wish they fix the no-sorting bug (its not even greyed out), and they could have the delete song and don't sync back option, that it self is really annoying for most people especially in the era of PC Free... Also why do i need to sync still? because i typically buy music from CD (way better quality) if iTunes start to offer lossless i'll consider it 😝