Did you do a clean install? If yes, did you have any crashes afterward? I'm wondering if maybe this is happening as part of the upgrade (Yosemite -> El Capitan) and need to cleanly install the OS.
Yes, "clean" in this sense:
- Format both of my internal drives with Disk Utility from the Mavericks boot disk. I use the Mavericks boot because I hate the lobotomized El Cap DU and Yosemite's always gave me issues with turning the SSD into a "logical volume group".
- Do SMC and PRAM resets.
- Boot it from an external drive with El Cap installed and then initiate the installation onto my internal SSD from there. For whatever reason, I can't install straight from the bootable installer (get that stupid endless LanguageChooser error on both of my machines).
I haven't had a crash or any kernel panics that I can recall. A few hard reboots and lengthy shutdowns but nothing that's bothering me too much (OS X seems to be quite inconsistent with reboot times in my experience). I can't remember what I did with the no pinwheel freeze. It was odd; the keyboard and trackpad wouldn't respond yet the clock was still ticking so I hesitate to call it a "true" freeze. My current (and hopefully final) reinstallation has been behaving well, so far.
I'm no expert - I'm technically inclined and tend to fly by the seat of my pants - but I might suggest that you try a clean install. If you have the available space, make a separate partition on your internal drive and install it there. Then if you don't like the way it runs it's as simple as erasing/removing that partition.
This is like going back to Win95, "re-install" is the standard mac answer/fix these days.
The quality of the OS suck and blows at the same time
Maybe that's the working title for OS X 10.12 - Shop Vac - "The world's most versatile OS"
I'm an ex Windows user (~1996-2008; prior to which I was familiar with Systems 6 & 7) and somewhat OCD, so take those two together and clean installs are what I prefer. I've never done an "upgrade" of OS X - I might have the first time I ever upgraded, Leopard to Snow Leopard) but if I did I probably reinstalled clean not too long after.
But I agree; I've been noticing over the past few years how Apple is becoming what Microsoft always has been. I'm sure Steve Jobs is rolling over with their capitulation to that way of doing things.