#4 They have lost the US education market to Chromebooks despite the very very late in the game attempt to claw it back with the lower cost iPad.
This.
The lack of traction of iPads in the education market has to be one of the biggest failures under Tim Cook's watch. This could bite them for years to come, and has to be one of the main under-reported reasons why iPad sales are falling.
It started with the complete bungling of iBooks Author, which could have been an ideal way to get modern textbooks specifically designed for iPads. This alone would have helped solidify a certain role for iPads in education, and help with regular, yearly, continued updates.
Apple also didn't truly understand the education market. You can't sell an expensive device to school systems with limited budgets where students can easily break them, lose them, or have them stolen. What this market wants are inexpensive laptops, with real keyboards, that could be easily maintained without an IT department. ChromeBooks came in and cleaned up. (And now Microsoft is trying to get in the game with Windows 10 S, software for the classroom, and cheap laptops from their OEMs.)
Apple is trying to make a comeback with Swift Playground and a lower price iPad, but I think its too little, too late. Google and Microsoft are playing the long game, trying to get students hooked on their systems early, duplicating what Apple did successfully with the Apple II decades ago.
I think Apple should create a new, 2 in 1 "iBook", which looks and acts like a clamshell laptop running iOS, but the screen can be detached and turned into an iPad. Price this right, along with a renewed focus to iBooks Author, Swift Playground, and maybe purchase somebody who makes software for education, and they can get back into growth mode.