Well, well, well. How history always seems to repeat itself.
Remember those times fiddling with system extensions back in the Mac OS 9 and earlier days? Some were fighting each other causing system freezes, crashes and odd behaviour in the middle of a session or at boot time. So you had to put them aside one by one to see which one was causing the problem. Well here we are again. No nice GUI with puzzle shaped icons this time, just raw command line language.
My old MacBook 2010 upgraded like a breeze from 10.9 to 10.11, however after 10.11.1 it got stuck at boot time. Verbose mode didn't give a hint what might be the problem. Reading in this post about the Eltima kext, which I didn't have btw, I moved all kext's older than mid 2014 aside in a Terminal session in recovery mode.
These were the bad guys for me:
System/Library/Extensions/USBExpressCardCantWake_Huawei.kext
System/Library/Extensions/Vodafone.kext
In Terminal type:
cd /Volumes/<your harddrive>/System/Library/Extensions
mkdir temp
mv <extension name> temp/
Automatic backup, system self repair, integrity protection, and other systems alike, to what avail if incompatibilities are not detected? Please Apple don't put us through that system extension **** again. Make OS X rock solid again.