Did update today an iPhone 5 32GB and an iPad "3" 64GB (= the first retina iPad) from 9.2.1 (with which they ran very smooth) to 9.3.1 with a success for both, but with an error at first try with the iPhone 5. After restarting it worked with the second try. It seems that the iPhone had already loaded (but not yet installed because I had unable automatic update for good reasons since a long time) 9.3 already some days and this blocked the update to the newer 9.3.1.
In addition I wanted just to install a SECURITY UPDATE for 9.2.1 - which was the only attempt at the very beginning.
It seems that this order of "upgrade-line" caused some "confusion" and led to the well-known frightening error-note.
At the end I accomplished nevertheless the update of the iPhone 5 and the update of the iPad 3 was no problem.
Remark:
Apple wants to force you to use iCloud:
Already the updates of two different iPhones from 7.1.2 to 9.2.1 and one iPhone 5s from 8.4 one month ago stopped with the step of activation of iCloud:
The "button" for activation is much larger than that of disactivation and the latter is at the very lowest point. That is not all: The space between the two "buttons" is very little - so you must really be careful if you want to tap on "Desactivation" .
This is topped by the fact that already one month ago the "button" to disactivate iCloud was NON_RESPONSIVE for at least 30-60 seconds. I tapped like a fool and NOTHING happened - while ALL other steps concerning other things than iCloud were perfectly responding!
This was all the same with all THREE different iPhones, so a hardware-problem can be absolutely excluded.
Today, it was even worst: The "button" was NON-RESPONSIV for at least 5 minutes!
Be aware: You have NO CHANCE to bypass this step.
After at least 5 minutes and getting more and more angry about apple playing the blacklister card it finally worked.
I find this really scandalous since I refuse any Cloud service and strictly backup only locally.
VERY BAD POLICY, apple !!!