At least when you get a duplicate for the Champion tier armor, you can take out the mods and put them in other armor, like getting a duplicate for a Champion helmet and taking out the (56) mods and putting them into Centurion tier gear.
What really sucks is when you get duplicates for stuff like belts or relics which become absolutely useless. I have 5 belts so far, 3 of which are being worn, and 2 that are just sitting in my inventory.