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I'm seeing conflicting things about restoring from a backup.

I currently have a 5s on iOS 9.2.1 and I'm interested in getting the SE, which will be on iOS 9.3, of course. I backed up using iTunes and loaded it on the 5s. It would be much easier for me to just restore that backup onto the SE, but not if it will cause issues. I have seen some say that it causes issues and others say that it doesn't for them. I prefer using iTunes though, to back up.

What's your experience? Do you backup and then restore, even with new iPhones, which have a new version of iOS? If I was to backup with iCloud, will I still run into issues?