I try to match my gravel with the color of food I am feeding them. The red food gives them red poop, which doesn't stand out on the gravel as badly.
One thing I did think about though was when I was looking up information on how to de-ick an aquarium, that in the protozoans lifecycle they will sink into the bottom for awhile before rising again to attack the fish. Does the gravel allow the Ick to survive easier, or does it allow the fish to handle the ick better since there is gravel to scratch upon or trap the ick?
Will a bare-bottom tank make it more difficult for the parasites to survive?