The first part of my idea is to remove dyes and recipes that create the same item as another recipe, but in a different color. And also to remove items listed more than once in the wards by different colors as it makes the lists long to scroll through.
Example: Cobalt Harness having a different recipe than the red version, when it's the same item, and both items being listed under war garbs.
The main idea of mine is to instead add a "Customize" option at the end of a craft, much like the touch up option, and with "Customize" allow a crafter to edit the color and trim of an item. If somebody wants to change the color you could add one universal type dye that can be used on all items like dark matter is used for repairs.
I recall the director expressing that he likes each player being unique, this would help players accomplish that. My linkshell colors are white and black, I think it would be awesome if our crafters could make all of our gear white and black (team colors).
For the wards you could make it so only the generic colors are listed (so there are less items to scroll through) and the player would have to see a crafter or npc to change the colors. Or you could have the generic item listed when it's selected a new list pops up of the main colors and then lists for trim colors.
Crafter signatures are a common request, "Customize" would also be a nice touch to make gear by crafters unique. I personally wouldn't want somebody to be able to change to colors on an item I've signed, so if this option and signatures both existed you could make it so you had to remove the signature if you wanted somebody other than the item's crafter to change the color.
I realize this would make it hard to "re-skin" items but I think it's a small sacrifice (People don't typically appreciate re-skinned armor anyway).
P.S. I can't remember everything that's been requested or is under development so if something is an old idea I apologize.