I have a 2012 Macbook Air. Ever since I upgraded to El Capitan I've had this problem. I thought the subsequent updates would eventually solve this problem, but they have not. It's driving me crazy.
A couple things: First, i do not have Fusion installed, and never had it. Secondly, I too would close the lid, wait a few seconds and try again, thinking that was the solution to unfreeze it. However, what I've discovered (for mine at least) is that I just need to let it sit for about 5–10 seconds before it unfreezes. That is, I realized it had nothing to do with closing my lid. I just open the lid and just try pushing a key every few seconds (for my password) until I see it's not longer frozen.
I did just delete the only saved Bluetooth device (a bluetooth speaker) that I haven't used in months and months. We'll see if that does anything at all.
On my 2010 Mac Mini, I haven't had a single problem. I don't have a password set on that machine, but I've never noticed it freezing after waking from sleep.