I'll be the other end of this and say I don't think it's fixable. I agree wholeheartedly with where the problems lie, but fixing the problems requires far more than just a design leader to control matters, that way leads to modern Hollywood and last second rewrites/reshoots of messes like Justice League.
The game is its sex scenes, the RPG is... it's a thing...
What SoulsSurvivor says of it needing a Design Leader to come in and clean things up, might have saved it back in the early days before we left the old woods, but now there is so much content, so many random and abandoned character threads, that would need drastic re-writes to bring into whatever line you wanted to toe that you're basically asking to remake over half the game.
As a thought experiment; try to make the game fit some form of logical, tight, story-telling, then consider how much content you've had to ignore or head-cannon to make fit.
Do this again, trying to find a perspective that would fit as much of the game's content as possible. And I think you unfortunately end up exactly where we are. A passive protagonist, bubble NPC's farting about with no regard for the plot, inconsistent world building.
It was rigged from the start, the rot set in young, remaking the game to be consistent would mean making a whole new game from the ashes of this one, and completely changing their production method from a collection of auteurs and bounty-writters, to getting work made for the plot. You'd lose the diverse content element that many like, as everyone wrote to demand rather than to their personal fetish.
Eh, at least it provides debate fodder, and so long as save editing and copium exist we can make our own stories out of this mess.
That's what you get for inviting two people who are the equivalent of malicious STD spreaders to your home.
In case people don't get it, the pair of them are demonic rapists, and everyone they have sex with gains corruption, to the extreme of losing their souls. They know this, they don't care, the world is a better place with their heads on spikes.