I don't think it is related to El Capitan specifically.
My laptop:
Macbook Pro Retina SSD mid 2014
Mavericks 10.9.5
It initially all started with the internal trackpad not working on waking about 2 months ago. Now if I close the lid for more that a few minutes the keyboard freezes on opening the lid. My bluetooth mouse works fine but I can't log in because of the keyboard. The caps lock button doesn't light. The only key that will work is the power button. The only way to get the keyboard responsive again is to do a hard reboot. The trackpad very rarely works now and I'm forced to use my bluetooth mouse. So I suspect the keyboard issue is related to hibernation. Heaven only knows why the trackpad will not work.
So every time I finish with the computer I have to shutdown and to reboot to use. I'm certainly glad that this will only take about 20 sec.
I have Parallels loaded and will occasionally use a window 8.1 virtual machine. Interestingly if a close the lid and reopen it with windows 8.1 going the trackpad will occasionally works fine, but this is very sporadic and most of the time I can't replicate it.
I do not think it is a hardware issue though rebooting in safe mode will not make my trackpad responsive.
I have tried all of the suggestions in this tread but nothing has helped.
Somehow I don't think taking my laptop in and getting the trackpad fixed or replaced will help, especially since the trackpad will work perfectly from time to time.
Paul