Global economy needs to be modified. Something simple like a "priority" system on cities where you tell the population what to focus on (therefore, making the city giving more of resource A but less of resource B and C) would already give cities more meaning. Or even something like a global budget system that decides wether you want to focus on a resource or another.
Right now, all you do is build. Make 10000 cities and build, build, and build even more. There is no strategy, just mindless building, because there is barely any strategy.
And why would they allow a city to have a study, an arcane study and a market at level 1? By doing that I can just spam lvl 1 cities and gain a crapload of resources. Also, having to build barracks to train units should be brought back. Global technologies is one thing, but not so much when it applies inmediatly to all cities... I mean, why the hell can I build WHITE SPARKLEY PALADINS OF MIGHT on my lvl 1 village? Come on, Stardock, you know better than this, remember all those great strategy mechanics you used in Galactic Civilizations...
Now, what I'm saying is, building cities should be something COSTLY and RARE, and therefore, CITIES themselves should be MUCH MORE IMPORTANT that way. Pioneers should be expensive and take long time to build. Hell, at least, unit building speed should be determined by the city size AND it's military buildings.
Okay, let's say I CAN build WHITE SPARKEY PALADINS OF MIGHT on my lvl 1 crap town, because I have the knowledge, but at the least, make it so it takes a lot of turns to do so, compared to the time it'd take to train them on my advanced capital.
I know you are taking a different approach for this game, with the RPG elements and all, but remember how GOOD you are at making strategy games, and use that to give this game some shape. I know you can do it, you're a great company, and I wouldn't want all the potential this game has, which is ENORMOUS, to be wasted.