Hi,
I have been having this same issue for well over a month ever since I upgraded my 2011 17" MacBookPro to El Capitan. I was getting random freeze ups which could only be solved by forcing a shutdown and restarting. Often, I'd have to restart multiple times to get the system back up. I've never had any issues with my Mac and ran countless diagnostics trying to isolate the issue - nothing. I finally found a forum that mentioned El Capitan being the possible issue so I just downgraded to Yosemite last night and have not had the issue since.
To be clear, the only resolution to this issue is to downgrade to Yosemite. Reinstalling El Capitan (short of a fix from Apple) is NOT going to resolve your issue. Until last night, I haven't been able to do a clean start/restart since shortly after installing El Capitan. The first restart after I deleted the drive El Capitan was running on was clean and all since have been clean. I've had no lockups or freezes either.
Apple needs to stop dancing around this issue and fix it. For the first time in 6 years, I am actually contemplating going back to a PC between issues with Apple Operating systems and the absence of a 17" machine in their lineup. I was so relieved to find that the issue was just the new OS and not my hardware since I REALLY do not want to go down to a 15" system.