Upgrade to El Capitan, unable to use keyboard and trackpad after sleep
Ok I can confirm that the keyboard and trackpad are stuck after sleep when I let VMWare Fusion running... If you have something similar that's running in background it could be the problem.

To resolve it at the moment I pause all Virtual Machines and everything goes alright now.

This is probably related to kernel modules installed by VMWare but I can't find any clue...