I think the biggest things to take away from this response is that Origin of Powers is an arc told from the point of view characters in the world of City of Heroes, and they don't really know what's truly going on. Because of this, the TRUE nature of the origin of powers will be revealed to players later, restoring what most of us think of as the "proper" origin of powers - namely, our characters. .....or something like that.
While that might have been their intent - and different developers have different intents - that's not what the later stories about Incarnates and the Well explicitly stated, and would have been difficult to retcon. Even after Origin of Power's fuzzy, annoying, and scattershot aspects were complained about, their remedies for that if anything tried to help a drowning man by setting him on fire. Prometheus, who is supposed to know the story we don't yet, and in what legal minds might refer to a "excited utterances" refers to the Well as something more than just an amorphous construct, Prometheus is seen to hate the Well, as if it was an entity and not a mere reflection of human potential. The Well is given a personality. And it is shown capable of taking over other beings, like Statesman and Recluse.
I believe those developers were sincere, but I believe in this case they were also wrong, even about their own intentions. And regardless, the wheel of mmo development often grinds independently of intent, with the momentum of cumulative contribution often overriding individual developer's intentions.
The exact, precise, word-for-word way the Battalion were going to try to demolish us was really going to be their last chance to rectify all of this, and I have my doubts they would have. I think they were trying to do too much with the Battalion, and it was going to paint them into narrative corners, again. For an extremely powerful destroyer of worlds and species and something Prometheus believes an Incarnate army of the caliber of Emperor Cole's was totally incapable of dealing with, the Battalion seemed content to use spies and front men to do their dirty work for them. If they needed that sort of deception and subterfuge, the odds are they could not really be the big bad incarnate-crushers they were being built up to be. Doing all of that allowed the devs to turn the Coming Storm into a power play story before the actual shooting started, but that stretches the narrative out at the expense of diluting it greatly.
And that would have made it very difficult to salvage Origin of Power/Incarnates. To be a threat to the very existence of Incarnate power, the Battalion could not possibly be entities that fought at that level. They had to be cosmic threats, fighting on planes vastly above such matters. A politician and a spy cannot dismantle the Well of Furies if the Well is a reflection of human potential. That would be like Back Ally Brawler trying to punch the concept of Sadness into submission. Sure, its just comic books so you can Deus Ex Machina all you want. But when the end game is bringing in Rularuu, destroyer of dimensions on your side, the enemy cannot be Cobra Commander.
When Galactus comes for you, he doesn't send spies, he doesn't send scouts, he sends a Herald. And the Herald is not there to spy on you, he's not there to bargain with you, he's not even there to fight you. He's there to ring the dinner bell.
If the true origin of power is actually inside us and not something externally powering us, then there's no way to steal that potential from us, except by taking it from all of us individually. Like, say, by enslaving an entire race of beings and using their life force to power your warp drives. We can't be cheated of it, or forced to give it away.
I get the feeling from the Lore answers that at least some of the devs felt we were too harsh on some of the build up stories, because we lacked the context to interpret what was happening correctly. That can be true sometimes, but I don't believe its true in this case, at least for me. I believe the narrative direction wasn't ambiguous, and was thus going to be extremely difficult to reverse. And at best, you might try, and end up with a twenty car pile up of ideas smashing into each other.
After the Coming Storm and the entire Incarnate story, I believe the entire thing was going to be nullified (narratively) by Ascendancy. The clean slate that told the players that the path to power was individual and self-controlled was going to be Ascension.