First, I want to congratulate you on delving into the Deep like you did.
Second, I see the story as a battle between Light (the Sky) and Dark (the Deep). The two opposing forces are trying to shape the universe into a final shape. The Sky attempts Order through Golden Age utopia. The Deep attempts Chaos via dystopian genocide.
Their agents? The Sky has the Traveler, the Deep has the Worms (whom employ the Hive).
We know that the Traveler visited many worlds bringing Golden Ages, but it is only on Earth that it raised Guardians.
The power of the Deep feeds off of Light, and even transforms it (all lower Hive tribute the Light they consume to higher ascendants until it finally reaches Oryx and his sisters to tithe to the worms).
So here is the kicker: Guardians are the Light equivalent of Taken.
Just my theory.
While I agree that both sides are fighting to attain a particular kind of universe or Final Shape, I don't think it furthers the discussion on the specific Final Shape sought by the Darkness.
The Final Shape sought is likely conceptual. As the Worms are agents of the Deep, I doubt they are truly privy to the Deep's actual desires, assuming it is even sentient. The Deep may simply be the Worm's god of chaos. They may be trying to bring about a universal collapse (if the universe fell into itself, it would eventually explode again).