In the isolating chaos of the underground, there is logic! Station color groupings depend on the line's orientation in relation to Manhattan. All stations in the general "family" of an area, regardless of train line, follow this color scheme, varying slightly in hue between each group.
The shift in color group happens at each express station, presumably to help a rider intuitively look up, and facilitate their transfer. By this logic you should be able to look up, and have a vague sense of where you are.
I had taken this train twice a day, most days of my life since the age of 11, and never stopped to question it. All these years I have wondered just how is it that I've been able to fall asleep for most of my ride, wake up, and jump off at just the right time and place.