Since the beginning, it’s been the case that when you restore a backup of an iOS device from iTunes, it doesn’t restore the apps as part of the backup. That makes sense in some ways - the app data is completely separate from your personal data, and the apps can always be restored from the store. In the past, this has always worked fine for me, and in the past few revisions of the OS, it’s even flawlessly maintained the position of all of the apps I had installed. With the advent of encrypted backups, it’s even stored saved passwords with the backups. This is good - the idea of restoring from a backup is to get you back to exactly where you left off in as little time as possible.
But this time around, there’s a new wrinkle. Without fully realizing the implications of that choice, on my last iPad, I had turned off the syncing of apps with iTunes in favor of managing the apps directly on the device. That seemed like a rational choice at the time - there was little reason to manage my apps in iTunes when I could just as easily do it on the iPad. However, as it turns out, if you have app syncing off, and then restore from an iTunes backup, what happens is this: you get a freshly restored iPad with all of your data, and exactly zero apps installed. Apparently, the ONLY way to get them back is to painstakingly go through your purchased list, figure out what you actually had installed, and bring them back one by one. And if you happen to forget something, you can end up with a lot of orphaned data in your Other section where the app’s data still exists on your iPad but the app doesn’t (the only way to delete that data is to magically figure out which app it might be, reinstall it, and then delete it again). Moreover, once you turn off sync apps, there’s no evident way to turn it back on again without completely wiping the list of apps that are already on your device and starting fresh. With a few hundred apps, this is a world of hate. [Update: some recent version of iTunes seems to have re-enabled sync apps by default if you had it turned off before, possibly because I complained about this problem. I’m not sure if this is fixed universally.]
Incidentally, restoring from an iCloud backup does do the post-restore app sync, but with two important differences: 1) it throws a large number of “restore incomplete: some items could not be restored” errors with no information about what actually failed, which is not very confidence inspiring and 2) it does not store most passwords. This last is a nice security issue if someone happens to get access to your backups, I guess, but it is hardly what I want out of restoring a backup. What I want is to get back to where I was without a lot of effort. Previously, restoring from an encrypted iTunes backup was the best way to do this, but it’s now hopelessly broken if you take advantage of the iCloud features of starting to separate from iTunes. (Update: A number of people have asked what I’d like to see here. The ideal solution for me would be to have the saved passwords stored with the iCloud backups, but encrypted separately with a different password/pass phrase, with no recovery option for that separate password. If you lose the password password, then you can still recover your backups, but your saved passwords are gone and have to be re-entered. That’s a hassle of course, but it leaves you in no worse a situation than is the default now with iCloud backups.)
Apple is trying to push people towards the cloud, which is fine when it works, but this is a very big functional hole they’ve left open. I’m disappointed in the user experience here. iCloud suffers from a large number of these kinds of transitionary elements where it’s not sure what it wants to be or how to get there. It’s time to rip off the bandaid.