I love everything about ios, iphone, and my ipad...except iTunes. It's an awful experience, particularly after ios5. My view of Apple is changing slightly now. This experience I'm sharing below has a Microsoftish feel to it.
Why it's such a nightmare:
1) In order to update to ios5, you really have not much choice but to sync apps, otherwise you have to do a lot of manual re-downloading and re-sorting/repositioning.
2) I want to stop syncing with iTunes and instead sync with iCloud. However, by syncing 127 apps, there's no way I can backup to iCloud without paying for extra space. 5gb is not even close to enough space. Why should I pay for the extra space when the apps are already stored on Apple's cloud anyway?
3) So naturally I tried "un-syncing" the apps. And of course it says it will delete everything on the iphone. Why does it require this? How does it benefit me, the user? Who is going to want to delete ALL their app, but seriously? If I wanted to delete apps I could do it manually. Anyway, I went through the exercise just so I could really know (backing up beforehand). Surely enough every app got deleted. Then I tried a restore from backup. It restored only the basics, not the apps. It then automatically began re-syncing the apps with iTunes; thankfully it at least remembered the positons and folders. So, my conclusion is that once you check the "sync apps" box there is no way to ever un-sync after that without deleting all apps and their data from the iphone.
And, what iTunes calls "sync apps" is really not a sync. For example, if I delete apps on my iphone, it won't delete them in iTunes...even worse, when I sync, it re-downloads them on my iphone! I agree with RSAustin completely...the phone should be in priority position. I don't use apps on my friggin laptop. I only use itunes because I'm forced to if I want to put photos and music on my iphone. There's strange lack of logic here. I can see no point...no point AT ALL for syncing apps. I do see the need to remember app position and folder.
The fact that I can't backup to icloud without paying extra for more space is what feels Microsofty...like "haha we got ya now". I mean there is no way that Apple would not have known this would happen. How many of us have over 5gb of apps? I hope there is something I am missing here. If anyone has the magic answer please let me know. Otherwise I would say the Apple magic is losing its luster. I'm not going to pay $100 per year to Apple AND Dropbox. Dropbox is way more useful. Help!