The problem is that any 'iSync' app would still need to give you a UI to show you your media library contents (which essentially means the contents of your iTunes library). So, under the hood it would be the same library and the 'library manager' would need to run faceless in the background as part of the OS. And if you ripped a movie, you'd still need to open iTunes (or 'iMedia' or 'iVideos') first, add the movie to your 'media library' and then go to 'iSync' and sync it from there.I understand your point of view. However, I still think iTunes is bloated with features that stopped making sense long ago. iTunes syncing iPods back in 2002 was reasonable. However now you have books, apps, photos, etc on devices that are not music-centric. It would have been better to move devices out of iTunes into a dedicated program.
Maybe things would be easier and cleaner if you had an iAudio (music, podcasts, audiobooks, radio), an iVideo (movies, TV shows, home movies), an iApps (iOS apps), and an iSync app. A few elements of this exist already, before Photostream and iCloud Photo Library, iTunes was (and still can be) used to sync photos to iOS devices that were kept by other media libraries (iPhoto or Aperture). I always found this to be rather clunky, there is/was no visual preview (like we have, eg, with movie covers). An example where things work better is syncing eBooks, which started out as a category within iTunes and then got their own app on OS X and the syncing UI in iTunes looks the same as it does for movies, TV shows or other categories still managed by iTunes.
There are also a number of preference settings that currently apply to all content stored by iTunes that would need to be duplicated in each separate app (eg, in regard to library sharing, the Store, parental control). Logging into the Store would either have to be done in each app separately (iAudio for music purchases, iVideo for movie purchases, iApps for app purchases, etc.) or be done on a system level (eg, in System Preferences) as it is done in iOS (where I find it a bit annoying that I have to leave, eg, the App Store app to log in and out of different accounts). Also, currently, if I am in the iOS App Store, I can directly switch to iTunes Music Store without having to switch applications. I know, one could hive off all stores into an extra app but then the switching from the App Store to 'My Apps' would meaning switching applications. No matter how you slice things, there are advantages to have everything under one roof.
Apple also still sells non-iOS iPods (iPod nano and iPod shuffle) and even once it stopped selling those, a significant number of people would keep using their (non-iOS) iPods for years to come. Splitting music management and iPod syncing into two applications would very likely be not appreciated by their users.
I actually find iCloud Photo Library and iBooks where syncing is done (or at least can be can be done) entirely via the cloud a better solution than separating sync into a separate app. For sure, the size of synced items involved makes this much easier for eBooks than for movies. In fact there seems to exist some sort of iTunes Match for stuff in iBooks; when I add a pdf to iBooks on one device, it seems to show up on other devices as an optional download.
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