Things would start to make sense when you realize Aria was added to have the captive princess NPC the lore was talking about, then her questline was delayed to rework the house massively, then her Rebellion questline was introduced before several other mechanics were added. Even Clea was added after the NWO questline was completed. So even in this case, just one NPC, reworking her backwards into the NWO chain to make it more alive and interconnected would mean reworking parts of the quest chain. That is not even including the Senate, which was added way after NWO, I suspect partly because some players wanted to do things, rule things, have a prestige title as close to being called Chancellor as possible.
Oh, it makes sense that things are disjointed and anemic given the production/development history of the game. Whenever things are added in piecemeal or as afterthoughts, it's going to be a gordian knot to try and get them to work together. And I'm not expecting anyone doing a game like this to have a completely mapped out plot for everything in their game. Even if they did, that wouldn't necessarily be a good thing either, and lots of it probably wouldn't survive all the way to the final version without some level of rework. I was never under the illusion that you could just insert a scene with Arizona or Clea into the middle without a care. That's clearly going to be several wrenches in various gears. I mean, one of the things I suggested is alternate ways to join the revolution or acquire Aria. Obviously that's not going to play well with the quest as it currently exists.
Like I said, I'm not expecting any of the ideas in my outline to be implemented, because I understand that it's a massive rework of the questline. I think it'd be much for the better from both narrative and gameplay perspectives, as it gives you something to do other than watch numbers go up/down while you try to progress through the questline, but at the end of the day there's the reality of trying to make a game as a career. Plenty of games have been torpedoed by a dev deciding to continuously tinker or rework an element to their project, and I can respect a dev deciding that good enough is good enough and moving on to another aspect of the game. I may disagree about whether a system/questline actually is good enough, but I think that even if money was no object, and I had comparable skill to Grim as a game designer (which I obviously don't have), we'd have different ethoses and design philosophies, which would lead to different priorities.
To me, the NWO/SMR questlines seem like the obvious spine of the game. I mean, one basically share's its name with the game, and either questline is basically designed to lead to the answer of who are the "Masters of Raana" that you will accept? So it makes sense to me that these would be the most robust parts of the game. Both from the standpoint that since they're the most important questlines of the game, they should be the most developed, but also because of that, it makes sense that they'd be something of the main hub for expanding the world. Definitely not the only hub, but the main one that has the most reach to show you the world to help influence your decisions.