My iphone 4 was backing up to the cloud. I got a 5, and did the entire restore process. I was irritated and inconvenienced to discover that my email account passwords and my google 2-step verification tokens in the google authenticator app did not come back from the backup. I had to re-enter account passwords, and then tear down and re-set-up the google authenticator tokens.
Aside from my mild pique that the Apple person who sold me the phone neglected to mention this little bit of entertainment, I'm left wondering: is there any way to get backups to include this stuff? Do itunes backups include this stuff, so that I'd be happier if I switched from cloud to itunes?