Agreed. Syncing in a regular iPod was ok, but it used to be a bitch on my iPod touch because of it always wanting to back up the apps. What I didn’t get was, it insisted on backing this up in some library folder rather than the iTunes folder. Which is fine for small preferences files but not for apps that store real files like books or videos. My internal hard rive doesn’t have space for that. It should just all be in iTunes, and work the same way other iTunes files are synced. Plus that part of the sync took forever.
I’m just glad that the iOS updates through the cloud now. It’s much quicker and less buggy.
The files in iTunes ARE on your hard drive unless you specify that it should keep them elsewhere. iTunes isn’t magical in that it has a special place “in itunes” that isn’t on your computer.
Of course, I hear that with iCloud, that might be a little different moving forward.