I'm experiencing the same problem with my MacMini6,2. I have a 128GB SSD, 16GB RAM, and ever since upgrading to Yosemite I've been experiencing serious graphics issues. It's like the Intel HD Graphics 4000 1024 MB in it has driver issues or something. Here's a list of things I've experienced that never happened in Mavericks:
1. Boot chimes, but the screen stays black. A reboot often times fixes this.
2. Boot chimes, screen turns grey and two apples show up side by side toward the top entirely pixelated with pixelated progress bars beneath each.
3. Boot chimes, screen stays black and after 90 seconds(ish) the screen stays black but a white progress bar can be seen in a box (no apple logo).
4. Boot chimes, screen loads like normal, but when trying to login, the screen shows up, but the cursor doesn't and the dots representing the login characters appear like they are highlighted in light blue.
5. Boot chimes, everything seems normal, but as you're logging in, you see a line slowly descending horizontally on the screen adding extra detail to the screen. In my mind, I always think it's the GPU playing catchup.
6. After being fully logged in, I have my desktop set to change every minute. I like variety. When the screen goes to a new image, the whole screen flickers and various parts of the two images can be seen simultaneously as horizontal bands. This also occurs within any window of any app that's open. Things are also seriously lagged. When this happens, the rounded corners on every window aren't rounded, they show up as light blue squares, or sometimes black squares.
That's the best description I can give of the things I'm experiencing with my MacMini6,2. I've never had these issues before, and they aren't constant. To remedy this, I run Onyx and reboot. Sometimes that works, sometimes it doesn't. Sometimes, I have to shut it down, wait a minute and turn it back on. Basically, the only way to not go crazy is to wait for one of the many reboots to be a good boot and then never, ever, reboot the thing.
I'm not sure what happened to the drivers of the Intel HD Graphics 4000 1024 MB in Yosemite, but something happened. Something extremely annoying.