The answer is simply that you're not making sensible use of the available dimensions. Pink can be made to fit in (a) between red and mauve (which fits between pink and purple:), provided that you're willing to arrange your pens in a circle or (b) beside red on a two dimensional arrangement with hue on one axis and (saturation&value) on the other. Mind you, that pen-holder did occupy about half of my desk, and it was hell getting anyone else to put the things back in the right place.
Pen-sorting: you're doing it wrong