I see where you're coming from, and I'm not going to pretend to know the expenses and costs of developing a new game. However, it's probably fair to say that as a computer game company a fair chunk of their resources are devoted to research and development.
Maybe they should tear up the manual and approach the problem at a high level, if only in an exploratory way to overcome the limitations of the current paradigm. And there are limitations.
Let me give you an example. I am a secondary school teacher, and as part of an end of term activity I got group (10-16) of kids aged between 11 and 14, girls and boys, playing CIV TOT each day of this week. They could play individually or in multiplayer. They enjoyed it greatly, although it left virtually (if not totally) all the girls cold. And after a while I sensed they responded to its depth and gameplay. Yet when they see a fish Icon, do they connect it with a fish resource as a parallel to fish in the sea? I don't think so. They would ask "how do I eat that fish, sir?". when they see a settler on the land, do they see one or is it representative of 10,000. I think they see a guy in a park. Another thing a few of them asked was "when can I build bridges" and I would ask "why" and they would tell me they want to build a bridge over a "sea" between two land masses. I explained that that sea possibly represents the size of the english channel.
My point is this, while they enjoyed it and had a lot of fun, which as you rightly point out is what it is all about, their experience was still highly abstracted from what civilisation actually involves. And yes, I do have a problem with that.
I think a high level discussion on the aim of civ etc, is viable and necessary for the future sucess of the franchise.