I blame the writers for not thinking ahead. The Cipher was (on the surface) a cool mystery to explore. ME2 showed it wasn't, it was a "nonsensical plot device" as you call it, to be discarded when they were done with it. Would it be so nonsensical if the Cipher was something that was actually explored further, and played a crucial role in the story? Was Gollum a contrivance in Lord of the Rings?
It was always a nonsensical plot device, though, as in it made zero sense in application yet was absolutely crucial to that narrative. You're just giving it a pass as a "cool mystery" to become a cool mystery for later, when there's absolutely nothing indicating it would become this cool mystery. Again: "...explaining color to a creature without eyes". The mystery pretty much died with the Thorian.
There's a big difference between elaborating on the back-story of a character and retroactively making a magic plot device make sense.
I was actually looking forward to possible explanations for the Lazarus Project in ME3. Sadly all we got was "Derp, the helmet kept the brain intact!"
Sounds like you were once again waiting for a future installment to make sense of a poorly-explained current plot element. That's on you, and it shows how similar the Cipher really is to Project Lazarus (which makes sense since Karpyshyn is responsible for both). At least those audio logs touched on some of those issues, including giving Shepard a window to contemplate their existence.
Me3 was actually called that.
Commercials about serialized television shows say the same thing. I wouldn't trust those, either.