How can I assure that moving from a JB phone to non JB will be a smooth transition? Will I have to set up my 5s as a brand new iPhone since all my backups will be JB?
Do you play games? I always AppBackup to backup all my App Store apps. Then whenever a new jailbreak comes out, I install app backup from Cydia and restore all my App Store apps to their identical state. It's a pretty easy process if your comfortable saving one folder off the device to your computer. You can do this manually but it's a much more unloved and very tedious process.
It's an even more tedious process but you could always cook up a custom restore package with your game save data and restore from that (using iBackupbot). I'm sure there are other tools out there too
I personally don't care that much about game save data. And the ones I do seem to utilize some sort of cloud backup
To the OP: generally speaking, you won't have any problems. I would say it helps if you made a backup after you removed all your jailbreak tweaks though. The only problem I would really see is that all the jailbreak junk and clutter will be placed on the new phone with no way to selectively remove them
Meaning, you would have to start as new or cook up a custom restore package to remove the jailbreak junk or else your "other" would be higher than a non-jailbroken device
Yea that's the thing, some games use iCloud while others don't. App backup solves all those problems. Plus it can backup any App Store app so it's really useful. I like to back a handful of non-game apps as well. Then I jailbreak the new iOS and copy my AppBackup folder (it's actually called tarballz or something like that) to the device, and use app backup to restore them all to EXACTLY how they were before the restore. Snazzy little app haha.
I have a question in the same vein: I replaced my jb'd i4s with a new 5S & did a restore after backing up the old phone. Everything went fine for me & all my normal apps etc. were there. Once a jb comes out for iOS7 on the new devices, will backing my phone up again bring all my jb apps (SBSetting etc.) back, or will I have to redownload them all once again?