Thanks for starting this thread Tavrok - I feel I have understood some things better through reading this. Forgive my repeating bits to get at something more.
A sequence of odd things that have been niggling at me start with this passage:
Auriel-that-is-Akatosh returned to Mundex Arena from his dominion planet, signaling all Aedra to convene at a static meeting that would last outside of aurbic time. His sleek and silver vessel became a spike into the changing earth and the glimmerwinds of its impact warned any spirit that entered aura with it would become recorded-- that by consent of presence their actions here would last of a period unassailable, and would be so whatever might come later to these spirits, even if they rejoined the aether or succumbed willingly or by treachery to a sithite erasure. Thus could the Aedra and their cohorts truly covene in realness.
It sort of rings a bell with the 'disappearance' of the Dwemer.
And this bit too:
Those spirits that remained, lesser and greater, involuntary or eventual earthbone, surrendered all definite hold on divinity.
Basically it seems to say that the 'Gods' are not Gods ... we knew they could die - but this implies a lot more - I suppose you might say they are diminished - as Vivec described his fate when discussing options with the Nerevarine.
This next bit has some real bite too:
The powers also created Red Tower and the First Stone. This allowed the Mundus to exist without the full presence of the divine.
so knowing that those that remained would no longer be Gods or Divine as stated they had to replace the Divine - and that makes me think that the death of Lorkhan aka Shor was a ritual sacrifice rather than simple murder. But this makes a nonsense of an oft (here on the forums) stated mer position that they wish to undo the towers - because the mer built them:
As they were the most powerful of lesser spirits in the ages after the Convention and eager to emulate what they saw, the Aldmer began construction of their own towers. That they built more than one shows you that they were not of one mind.
The Aldmer began to split along cultural lines, on how best to spread creation and their parts in it. Each Tower that was built exemplified a separate accordance.
Therefore the mer that want to destroy the Towers are renegade - and always were.
If your mod is to address more than the past of this matter then I believe you have to ask 'which tower will next be threatened and by whom or what.
One more detail:
Auriel-that-is-Akatosh returned to Mundex Arena from his dominion planet, signaling all Aedra to convene at a static meeting that would last outside of aurbic time. His sleek and silver vessel became a spike into the changing earth
It appears that he arrived in a Void/space craft ... and so we must ask is that true of the mer? Are the mer 'space-travellers' and some wish to return to travelling in space?
If this route is followed far enough then we have Star Trek (poor old ship lost far beyond known space) and that old Space Odessy wassitsname TV series where Starbuck, Adama & co seek to return to Earth to find help re-interpreted - with an interesting addit - the mer do not really seem to know which star system or world it was they originally came from. But right now they are stuck in a sort of temporal trap that recycles them and everything else ...