iCloud restore takes forever

I had a very similar problem last night: did an encrypted iTunes backup of a 5S (as instructed by Apple Support in order to save workout data on a Watch). When I started to set up the new iPhone 6S from that backup, it got stuck after about an hour: all apps said "waiting" but nothing was installing. I called Apple Support, who told me it was because the encryption was taking a long time, and they'd call me back the next day. After 5 or 6 hours, I was fed up and canceled the sync, thinking I'd revert to an unencrypted backup if I lost everything. Well, the phone did not lose the stuff that had already installed, and the sync started loading apps again after I reconnected the phone to iTunes. BUT then it got hung up again, with a spinning wheel and "waiting for items to copy" message. I ended up stopping and restarting the sync about four or five times (even had to Force Quit iTunes one time) before all apps finally loaded. I reported it to Apple this morning, and they seemed baffled. So, if all else fails, try canceling the sync and restarting it.

If you are restoring from iCloud to a new phone over WiFi it can take up to 24-36 hours depending on how many apps and data there is to update. It has happened with me with every change since 3GS

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One more thought: all iCloud backups are encrypted, and Apple Support said encryption slows things down. I deliberately used an ITunes backup because I thought it would take less time. But, since Apple said I would lose workout and health data on Watch if I didn't encrypt the backup, I went ahead and encrypted the iTunes backup for the 6s. It may be true that encryption slows the works (and probably Wifi does too), but I think there is an additional glitch - the restore hangs up when loading apps that aren't part of iOS9. Apps say "waiting" but don't load and install. It was counterintuitive that stopping and re-starting the restore/sync would work, but it did. When the apps started loading after a restart, they loaded quickly until the process hung up again. Eventually I did get all data, photos, apps etc loaded, and the 6s is working fine, after a 6 or 7 hr ordeal. I have updated almost every iPhone (2, 3s, 4s, 5, 5s) from the first one, and this is the only setup/restore that was not quick and effortless.

This helped me... I remembered that I had an additional itunes store account in a different country (needed an app offered only in that gso). Once I logged in to that account (from the app store app), it completed the restore and offered me the iOS 9.0.2 upgrade. Thanks!!