With the connection now between iCloud, Apple apps on Mac and iThings (iPads or iPhones) and iTunes 11, Apple has made, in my experience now, things worse. They're pushing you to move to backing up everything on iCloud.
They're doing this by putting the iCloud as the default interface and backup and then making backup up through your Mac and iTunes tedious. They want to make it so you just set backups for anything automatic across platforms.
That's their plan and to some it's nice if you want iCloud to have everything you do. Think about that. Everything you do across platforms sitting on servers somewhere in the US, maybe, holding all that information you can't account for its security and privacy.
I found this today when I updated Apple Pages, Numbers and Keynote on my iPad through iTunes and then tried to manage the files on the apps on the iPad through iTunes. It doesn't work anymore to add, replace or delete files through iTunes.
First I went to delete an updated spreadsheet on the iPad through iTunes. It worked with iTunes 10, but it doesn't work through iTunes 11. I have to delete it from the list in iTunes and the manually from the iPad. The "Sync" doesn't delete anymore, unless you sync it through iCloud instead of your Mac.
And then I wanted to put the new file on the iPad, which before it would sync through iTunes. Not anymore. What you have to do is put the new file in iTunes for the app, sync the device(s), open the app on the iPad and then add it from the list from iTunes.
If I used iCloud, it would just to it automatically, but then two things would happen. I would lose my control of the sync in iTunes and a copy of the file would be in iCloud. If it was a files of personal stuff, that's not where you want a copy to reside.
I saw this with my iCloud e-mail account when iCloud automatically added it to my iPad even though I don't want it there and now can't delete it from the iPad without causing problems with my e-mail account in iCloud and maybe on my Mac.
I also see this in Apple apps on the Mac which have an iCloud link to automatically push new or updated files to iCloud and to other devices. You have to turn this default off or it will automatically do it with some apps.
In short, Apple is pushing iCloud to be your friend but it's Big Brother. Beware of it and what you do with it, and ask yourself do you really trust Apple's iCloud when it's just a big server somewhere they won't tell you and won't ensure your stuff is save and private.
This is the future of computers and work on them. Beware of what others do for you in the name of helping you do more. Beware.