What I've done to minimize the problem:
1. Reduced the brightness
2. Turned on Bold fonts (under accessibility)
3. Moved my commonly used apps out of folders and reduced my number of folders
4. I look away from the screen when I know the zoom transistions are coming.
I figured out the worst animation is the one right after login where the apps fly in in two distinct phases; the middle 4, pause, the remaining 10. This really throws me for a loop.
The biggest problem is that the animations are different depending upon where the app/folder that is being minimized is located, there is no brain anticipation that can help alleviate the problem, it's all "random" movement.