What if cities had to choose a path at level 2 similar to champions' "Path of the....".
This selection at level 2 could then determine the offerings during future city level ups and thereby create truly specialized cities.
Now, I actually quite like this, however I don't think it would work too well in addressing my OP issues, and would ultimately lead back to our current issue of not making any meaningful decisions.
So, for example, if I selected the 'Military' type for a City, then the buildings options I'd have would be restricted to this type. Even if they added additional buildings, my decisions are narrowed, not opened.
What I mean is: I know I'm going to want Military buildings in the city, and I know that I want it to produce more people for that purpose - and so will Stardock, and they'll design the path accordingly. What decisions am I then making? None - I made one decision for the whole of the City. It's done. It's a Military City - it needs to produce lots of people for training and lots of buildings to make better soliders. That's it. You could automate all City level decisions for that City, and generally speaking it would make the right decisions.
That's really quite boring in practice, although it sounds great in theory.
In my opinion, Cities should be able to evolve as you play.
Initially, your Capital is your "Be All City". Once you get your second City, you generally try and specalise a little at first - Military first, Research first, whatever. Your Capital is then shifted from "Do Everything" to "Build Military Units." Because that's all it can do - it can't focus on Research, or Magic, or Food production, or whatever - because there's no avenues in the game for this. It can't do anything else. In Civilization IV, it takes literally the entire length of the game to reach that point. In Fall Enchantress, it takes 3 hours.
The issue is that there aren't enough Turn to Turn decisions that have meaning at a City Level. You build all buildings in all Cities, then you make Military Units. That's literally it. You can't deviate from that - you can pick which order to build stuff, but you'll always follow that pattern. And, due to the nature of the level of the benefits provided from each buildings and limited nature of the diminishing impact stuff (Unrest, Taxes, etc.) you never really have to think about anything.
"What do I need?" is only relevant for the first two Cities. And it's a big issue, from my point of view.