it is a big mess by Apple, I cannot imagine that the company grown to big as they did and start (some time ago) to decline in quality of their delieved products. it is a big quention that started to roll in our minds, should we stop the OS X updatings? Yosemite was clearly the missing part of the Marverics and El Capitain is to complete the iOS adaptation of the OS X, they brought some new features YES, they brought also better performance YES, but the big question is, do we really need this? and when put it on the balance, is their value good enough for the troubles (hours lost and patience) they are causing?
until now I say yes, the updates until now deserve all the lost hours, but future updates? I am honastly thinking stopping right here on the 10.11.1 and thats it.
for this actual problem, be patient, the download file from the App Store is ok, make a duplicate of it on other location so that you don't have to re-download it. mostly important is that you backup your system before you start the update.
If your system hangs on the ± 3/4 of the progress status, don't panic,
1. turn of the computer, start in recovery mode (Apple+R) and recover your older system.
2. then advice, while running the older system, fo to Disk Utilities and do the First Aid to chack and repair your startup disk permissions.
3. re-install the update from the downloaded file and cross your fingers, if it works 🙂
if it not works, then next and best possibility is to do a clean install. build a 8GB USB stick with a installation 10.11.1 version. google it how to do it.
format your startup disk and install a fresh copy of the 10.11.1.
Of course, the main point on all these try-outs they will work IF YOU HAVE A BACKUP of your system, if not you are "dead".
Patience and persistence are also man righteous and necessery for reaching our personal life targets, but Apple be careful because the those virtues have limits