A 3D printer is, at heart, a prototyping machine. They will never be able to compete on volume alone.
What they can compete on is high-volume customization. Josef Prusa, the designer of the Prusa Mendel, wrote a Python script to automatically add a custom pair of initials to the many whistles he prints out as gifts.
The great thing about open source is that people do cool stuff like this and then give it away! You an download the WhistleGen program Josef Prusa wrote from his GitHub repository. Perhaps someone could modify it to take advantage of two-color or multi-color extruders.