The problem is that the game seems to want it both ways. It wants to be a game where economics and underlying systems are the real problem, where just taking over a city by force of arms doesn't solve the real problems, and where the Guild is a legitimate threat, but it doesn't want to actually provide any of the frameworks needed to have a GM manage any of that.
There was a thread on RPG.net where Stephenls was talking about the Hamilton musical, and how he was glad that 3E didn't have some abstracted management system because it wouldn't capture the experience of arguing about nationalizing the state debt, etc. He didn't really seem to consider the fact that, without a system, that conversation would never even happen at most tables, because neither the PCs nor the GM are knowledgable enough about economics to have any idea what such a plan would actually do, and without a system, there's really no reason to engage in that at all, because there's no way of assigning meaningful consequences to the actions players take.
Yeah, wanting things both ways is something that Exalted seems prone to, even in the previous edition(s).
As for the players and the GM not being knowledgeable enough . . . Well, I think that a system can't help with that. IME, if people are not knowledgeable enough for the things a system emulates, they just stare at it glazy-eyed, until they end up internalizing it as just a gamist thing; if they're more knowledgeable than that, they'll say the system is inadequate; if they
disagree with the knowledge based on which the subsystem was built (whether rightly or wrongly), they too will be disappointed. Sure,
having a subsystem is cool, but the question is largely whether the reward is worth the effort put into creating one. 1e didn't have a mass combat system, nor an organization-running system, nor a mass social combat system, and yet the complaint that 1e is worse of for this lack seems to be a rare one. (Similarly, the XP/BP split is part of the classic strain of Storyteller/WoD-derived systems, but it's 3e that gets flak for it.)
As a GM, I run GURPS, which has lots and lots of dedicated subsystems for all sorts of situations. Mass Combat? Got one. Spaceship/vehicle construction? Yep. Aerial dogfights? Sure! Inventing new technologies? Yes, and I am in fact using it over the last couple sessions. Managing organizations? Here it is (though I don't quite agree with the way it's written). Detailed rules for how effective
study is depending on various factors? There's a PDF for it. That's with a library of something like 10-50 PDFs, typically 32-300 pages each, depending on what is needed.
And yet, I keep running into questions that aren't covered by the system, such as how cheap should electrical power be given such-and-such cost and efficiency of power plants, how will the political leaders of neighbour-states
react to such-and-such military event, how did the evolution of such-and-such race go and what traits did this encourage. All these things can be made into parts of gameable subsystems; whether it would be desirable for a given campaign and party is hard to predict. For instance, in the Exalted campaign I played in, the GM (and other players) steered clear of anything that has to do with more than six people acting at a time (mass/social mass combat, organization-running, empire-building, trade etc.), focusing on the individual-scale adventuring; meanwhile, I was saddened by such avoidance, and was looking forward to Mass Combat and using Taboo-Inflicting Diatribe and Bureau-Rectifying Stick to fix city-scale problems (the two were related) and overall making an army/empire. The GM also didn't exactly like the idea of consequences being dictated by a gameable subsystem, while I would be totally okay with it.
So . . . I guess this leads
somewhere. This approach to subsystems and their absence, that is. Just not quite sure where to. Probably in the direction of more individual-scale heroism, I guess?
