I believe in setting up a more scientific process for figuring these things out. Changing a bunch of things and then claiming one thing solved the issue isn't something that can be claimed so I decided to start with one thing that has been talked about on this thread but I didn't see anyone try with the exception of people going back to Mavericks; I decided to replace my video driver while staying on Yosemite.
Alright, so if anyone here has ever caused their NVIDIA driver to crash on a Windows PC with drivers that had been updated anytime in the last couple years you would know that even when something crashes it usually doesn't lock up the machine. The screen might go blank for a few seconds but the driver will restart itself and then the picture will reappear. Sooooo...
I took the latest NVIDIA drivers (for Yosemite 10.10.1) for the Mac Pro and asked them nicely to install on my machine (An early 2013 Retina MacBook Pro) even though they normally wouldn't allow this. 😉 After they were installed I have tried to crash the machine intentionally and been completely unsuccessful. Prior to this change I had to use gfxCardStatus to force the graphics card to either be the Intel or NVIDIA one (just so long as it didn't allow dynamic switching) because it crashed CONSTANTLY. Now I am allowing the dynamic switching and my machine hasn't locked up even once.
What it _IS_ doing is crashing the driver even once in a while. Remember what I said about how the PC driver acted? Well, now I will be working and when the graphics card dynamically switches it will sometimes work but sometimes it'll cause the driver to crash. It seems almost like a coin toss, but the good thing is that now it correctly restarts the driver like the PC one does. So I'll get a flash on the screen where it'll go black for a second or two but then it's right back up and no freezing up and I don't lose any work, etc.
So in the end it looks like something as small as changing the driver version is enough to cause big changes in the behavior compared to what I was seeing before.
Sure, it's not perfect but I can tolerate it at least for a while.... and then if Apple hasn't fixed it I'll take the machine in and let them pay for a replacement.