I wish that I had a definitive fix for you, bit I don't. All that I can tell you is to keep experimenting and trying different things. iCloud backups became extremely unreliable and hit and miss for me when I updated to iOS 9 last fall. I spent the better part of one entire day, signing out of iCloud on all devices, deleting iCloud backups, resetting settings, force restarting, turning Wifi off and on, trying different WiFi networks, turning off Find my iPhone....everything that I could think of to try, I tried. Finally, and for no reason that I can explain, my iPhone and iPad decided to both backup with iCloud.
I Don't know why it worked, but it worked. It continued to work for me until the other day when I tried to backup again. I swore that I would not go through all of the contortions that I went through before in order to use iCloud. I never auto back up with iCloud or auto sync with iTunes. I always initiate my own backups and I initate the syncing process with iTunes. I was ready to give up because I use iTunes for backups and I sync on a regular basis. I was beginning to really get ticked off, but for reasons unknown, it just started working again.