Before I start, I'm sorry if this has been mentioned before in this thread, but this is my collective thought after skimming some of the ideas.
My thoughts on the food issue, which in turn affect city spamming:
-Get rid of the food resource tiles.
-Create something similar to the 'create settlement' button that would create the farm improvement on land near water, or create an irrigation system. Make it so that this improvement only generates 1x food (So you'd have to use four tiles for farming to create a mid-sized village) and can be pillaged.
-I know this sounds a lot like the civilization form. It is, but it's also the most realistically thought out way of creating food productions. Blizzard and Westwood didn't go after other RTS developers because their resource gathering systems were used in similar (Game mechanically speaking) ways, so I doubt that there would be any reason why this form of irrigation system would cause a problem.
-This would also mean that big cities would need more than just space for housing tiles, etc, but they would need surrounding areas. Housing and food should be separated. Many large cities were surrounded by acre upon acre of farmland. It kept the food supply and the farmers close so that when the cities were attacked, people could retreat inside for the siege.
-It would also mean that caravans would be required to grow isolated communities or to provide food to resource outposts (i.e. mining towns, etc). Say there's a resource node off in the hills but no viable farming solution, you'd have to run a caravan there not only to bring the resource back, but to bring food to the community.
-To add even more life, perhaps upgraded farming techs could lead to things like hill terracing like that in South America, cross country aqueducts that are visible on the 3d map, things like that.
-By creating a farmland type improvement, you add more use for civilian style units. Pioneers only appear in my game if I'm making a settlement. That would make them a pretty hefty target once I start multi-player. But if there's a reason to keep multiple pioneer units around, it means it's harder to guess what I'm doing, and even if they kill some, chances are I'll be able to survive because I'll still have one somewhere.
-You also add more viability to sieges. What is realistic about besieging a town that has a node or two inside that produces enough food to supply not only that town, but two others? The siege would never end until someone attacked each other. There's no wearing down of food stores. This would create a way to occupy (Or burn, it should be a choice) farm land that could not only affect the besieged city, but other cities.
-Tactical options created by separating food and housing would become much more in depth. Say your opponent has a heavily fortified coastal city that is walled in by mountains or hills, and it controls that one elemental shard you desire. But because housing and food would be separate, you could send in a spy unit (Something else I believe should be viable, having heroes spy for you as they are not in any particular uniform) to track the trade caravan, and then besiege the source of the city's food.
-Water-based trade and warfare expansion. This is something that is extremely lacking. It would allow food caravans to travel to small islands for resources as well, and create cause for blockades too.
-Perhaps add a fresh water resource? If there was a great cataclysm, freshwater and springs would be extremely important.
-As I said, if I were a sovereign, which is the premise of this game, any adventurer I hired for field work isn't going to be wearing a banner or a symbol of my kingdom. They would be hired for discreet work. Smuggling, spying, causing dissension.
-These changes would require not just simple tile and resource changing, but changes in the way the AI acts and processes its decisions. It would provide a chance to create an AI that can react based on more than it is now. The AI could more strategically plan its cities because it has to process things such as, "What areas have I explored that are large enough for a good food settlement and relatively close to here?" "Is it more viable to attack the food supply city or the population center?"
-A water resource would mean options to poison the water resource. Just saying.