The biggest disadvantage I see to color coding your running rigging is that you won't be able to get a discount for the bulk purchase of line. If you can use all the same line (if that is possible given the size of your sheaves, blocks, cleats, winches, etc.), you may be able to purchase a spool of line at discount. Also, by having alot of extra line about enables you to experiment with different rigging arrangements at minimal cost as well having plenty on hand to replace running rigging as needed. OTOH, you may need so little line that the bulk purchase of it may not really be much of a consideration in the grand scheme of things.