Some of you are saying: so don't use it, media monkey or some other program manages it just as well. That may be true, but its not the whole story. I'm talking about syncing with other apps not just with the iPod functionality in iPhone. What about syncing my calendar, or my contacts? Or syncing an application that reads and writes office documents? And look I've tried a bunch of stuff Media Monkey, Double Twist etc, and all of them either require some other BS (DT requires an account with them, it won't just run locally, MM actually requires an install of iTunes for the driver, DT may too). And I still have to have iTunes to back up my apps and data.
Additionally, nothing is seamless because APL tries to lock everything out, everything is going through some back door, its a kludge. Instead of one application to worry about I have two. APL needs to publish an interface and let people write to it for syncing, tune management, even sales of apps. Why couldn't the iTunes store let other apps access their content?