Why my iPhone 6s restore application and its user data by Internet even when I backup them by iTune? I got my iPhone 6s and transfered content from my old iPhone 5 by following Apple Support HT201269, and backup my iPhone 5 with iTunes. After I restored the backup to my iPhone 6s, it's seemed that 6s was reinstalling all my 3rd party Apps and restored its user data with Internet.

There are several questions that confused me:


Where is my Apps user data saved? In my iTunes backup or in my iCloud automatically? I found that all Apple's applications restored their data including settings, and some of 3rd Apps restored their user data, but some not. How does iTunes backup my all 3rd party Apps?
Whether or not I click "File > Devices > Transfer Purchases.", it seemed that iTunes backup would not save any app, and will re-download them from App Store after iOS restored. But I can find all my App backup in iTunes, it doesn't make any sense at all.
How can I backup all my Apps and all their user data from old iPhone to the new one? if I need always connect usb cable when iPhone re-download Apps?
If you backup to iTunes, then iTunes. If you set up iCloud backup, then iCloud. If you set up both, then both. Some 3rd party apps don't restore, as the developers may have specified that user files shouldn't be backed up.
iTunes keeps apps in a separate location than iOS backups. Apps don't get copied over each time you backup, as that would consume a lot of space
Backup your old device to iTunes or iCloud. Then when setting up your new iPhone, choose either restore from iTunes or iCloud (depending on which you backed up to).