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I think with app-thinning, you can't transfer apps anymore. So you have to download them within iTunes from the store (from your purchased page).

-Kevin
What if apps aren't available in the app store anymore? Is there no way to back them up from now on?
 
If the dev didn't take advantage of app thinning, then it's a non-issue.
 
If I backup/sync all of my photos to iPhoto and then setup my 6S Plus as new, can I get those photos back onto my phone? What about my contacts? Do those disappear too?

I'm not as concerned about losing my messages.
I don't know about iPhoto, but if you backup your photos in the iCloud photo library and your contacts on iCloud, they will be there if you sign into your iCloud account on your new phone.
If you're still using iPhoto, you should consider switch to the new Photos app, Apple is not supporting iPhoto anymore.
 
Does iTunes finally keep everything in the correct order, folders, etc. I've always done iCloud because it makes it appear exactly how it was on previous phone.
 
Does iTunes finally keep everything in the correct order, folders, etc. I've always done iCloud because it makes it appear exactly how it was on previous phone.

I'd like to know this as well. I want my icons to stay where I have them.
 
I still can't believe there is not a way to set up a new phone as new and import your health and achievement data separately. I prefer to set up a phone as new, it's just easier for me. But now I have to restore from a backup to save my watch and health data. I'm thinking I will go iCloud. It may take longer, but it restores only critical files. My iTunes backup is 400MB, while my iCloud is 150MB. I don't know what that extra 250MB is, but it's probably junk.
 
The back up on my PC with iTunes is from a old 5s about a year ago, so will most of the apps on there be outdated and need to be updated anyway?
 
If the dev didn't take advantage of app thinning, then it's a non-issue.

The developer doesn't control app thinning, the App Store does. You upload a full binary and all asset sizes for devices you support. The App Store determines your device and then slices the correct ARM binary and assets based on your device type.
 
I'd like to know this as well. I want my icons to stay where I have them.

It does. I recently had to do a restore with iOS9. Once you get through the somewhat painful process of downloading all of your apps and removing the ones you don't use, it's good from there.
Of note - apps that are no longer in the App Store will also get downloaded, so you can recover those too.
 
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