The loot system in HoW is complete trash, and Ciphers are the worst of the worst. Every person in my PoE group has had over 3 Ciphers drop, and every person has received more Ciphers than elemental primaries. There are 3 unique exotic weapons and 12 permutations of the fallen primaries which doesn't even include the fallen perks, so I'm not sure what is up with how backward the drop rates are.
On top of all that, I just got the glitch where a stupid Cipher dropped that I don't want or need since I have all 3 weapons already. However, I can't discard it or turn it in. Even if you don't complete Skolas 3 times every week, Ciphers are going to quickly become nothing but an annoyance until Bungie fixes the glitches associated with them.
And I haven't even touched on the awful Judgment's Chance system. The structure of the loot in HoW is a real step back, and I hope we get another contrite but misleading 'we learned from our mistakes' post before the next DLC so I can have at least some false hope that Bungie listens to the community in this regard.