A few ideas, without too much detail:
1. A system of resources where luxuries are specialized coins, foods are specialized breads, and production resources are specialized hammers. Both specialized and unspecialized resources can be traded between cities, at some cost. Food trading is limited by tech (ie refrigeration) and access (ie roads and railroads). Probably about 3-5 movement points is the most realistic number.
Any resource can be normally used interchangeably with its supertype (both a unit of gems and a coin provide a coin for the coffers); however, production resources can provide special bonuses. An item may require 5 units of iron (only normal hammers can be provided with hurry production) in addition to 50 hammers. A unit may also allow 1 unit of marble to count for 2 hammers, for example. Foods and luxuries would still produce bonus crosses and happy faces, respectively; the first unit would provide one cross/happy, three would produce two, six would produce three, and so on. Thus, trade and diversity is important.
Power would also function as a resource, with transmission lines as a new tile improvement. Various buildings would require power, and various buildings (coal, oil, nuclear plants) and improvements (hydro plant, wave plant, solar plant, windmill) would generate it. Power could be traded between cities without merchants and at no cost, so long as power lines connect them.
2. Specialists would do more than just produce resources. They would serve more unique roles. For example, each type of specialist would provide beakers toward a related field (you would be allowed to select one civilization advance from each field to research, and further select one field as primary). Thus, a society with many priests will gain religion advances faster, while a society with many scientists will get science advances faster, and a society with many artists will get cultural advances faster. Specialists will consume gold, as per the culture (artist) and science (all) settings for the civilization. The additional abilities of each specialist are as follows (balancing may be required):
* Scientists: Add beakers to the primary advance, regardless of field.
* Artists: Produce culture.
* Merchants: Increase max number of trade routes, influence spread of corporations (see below).
* Priests: Produce a little of everything, and promote the spread of state religion to nearby cities, or all religions in the city in the case of free religion. Add a bonus to production of religious buildings and units.
* Militia: Add a bonus to production of military units. Grant XP to military units.
* Engineers: Decrease the cost of hurry production, grant a bonus to the production of wonders.
* Citizen: Adds one unhappiness (they lack formal employment or sense of control over their economic lives).
3. Corporations: Function similarly to religions. They have an HQ which collects profits from all factories in various cities. Each corporate factory also provides a "Blue Collar Job", a slot for a specialist that functions like a citizen, but with an additional hammer and minus the unhappiness (with Syndicalist labor civic, one happiness, but less gold produced). Economy civics strongly affect civ relations with corps the way religion civics do with religions. Primitive societies don't have corporations. Civics may favor national corporations (ie, with HQ in civ), ban all but national corporations, ball -all- corporations (state property), or allow multinationals to freely operate. Switching to state property and confiscating the property of corps HQed in other civs will create something of a diplomatic penalty for a while.
4. Robotic labor would be available very late in the game (getting close to the 2050 range). Such laborers would only be able to replace tile workers, citizens, or blue collar workers, and would consume power instead of food. Though they would not create unhealthiness or directly create crowding unhappiness, if there are not sufficient specialist positions for the displaced humans, the unemployed human citizens will create unhappiness.
5. Miscellaneous:
* Wonders should always provide culture for the civ that built them, even if it has long been wiped off the map.
* More near future techs, in a variety of fields.
* Enable creation of beakers through destruction of enemy units (ie, if the victorious civ does not have the tech required to build the unit). Buildings sold or pillaged also create beakers.
* UUs from Warlord Academies, instead of for civs. Leads to less balance overall, although if you get a souped up swordsman from a Warlord you get late in game, that could suck, and I have no idea what to do about generic Warlords. Wonders are an alternate route, and more easily balance.
* Differentiate between political and cultural borders.