iBooks is the main app I use on my iPad Air 2. After updating to 9.3.1 I am experiencing the following:
* iBooks crashes continuously - only a shutdown and power up fixes this problem
* Books are now out of the order I put them in - in all folders
* PDF randomly refuse to open - I get a message telling me that it can't find the book using its numerical id number
* iBooks is extremely slow when books either epub or pdf do open
* Navigation to folders is sluggish
* PDFs that I deleted are still appearing, but won't open
* Sometimes I cannot delete books
I am very disappointed that that Apple did not test this functionality thoroughly before releasing this version.
I expect that a fix will be provided but I am guessing that I will need to go reorganize all my books again in the order I want them to reappear. I have done this before in an earlier buggy release and it is a PAIN.
Lesson learned is do not update when a new release is announced, especially before a trip, - wait for the first adopters to report on the bugs. For all intents and purposes my iPad is now a brick. Very sad.