Era limitation is easily modded. Test of Time like stuff (the layers of maps) would be great and is NOT easily modded. Also a Sim City like element, depending on civics, of basically zoning and letting civilians build. Civ 4 was not a complete bummer, it has many good qualities that were not in Civ 3, especially the BtS version. Civ just has such a potential to be the one in all game. The philosophy of having to take things out to put them in is understandable in light of some of the overly-complex-up-front games that are out there. However, Civ 4 has all this stuff that's just invisible and uncontrollable and uncalculable. The surface layer should be instantly playable, and micromanagement should be there aplenty as you delve further. With that approach you can add without taking away.
Any discussion of changes instantly comes to moddability. You can skip all "this feature should be in" and "that feature should be in" by simply saying make it moddable. All the code should be utterly documented with modding in mind, saying exactly what everything does so there doesn't have to be a Wiki of discoveries.
However, saying "make it moddable" is not a comprehensive suggestion for the game for non modders. A tactical subscreen would be great. When stack A meets stack B in square (34,90), instead of watching what we do now, a new screen pops up showing the battlefield, square (34,90), with all the units of stack A and of stack B. Now archers can shoot over the heads of spearmen, catapults can attack the city out of range of archer attack, cavalry can flank. It can still be turn based, but tactical capabilities can be dealt with much better.
If possible, you could break populations down by skills, with each skill being a technology. You have the technology because you have a population who has that skill. So, you have X number of Agriculture technicians, X number of Iron Working technicians, and so on. Under the right conditions there is a chance a technician will acquire a skill for which their current skill is a "prerequisite," and you have a "Discoverer" unit/citizen. This discoverer can teach, write a book start a school, whatever. Additional techs might include things like Stone Age Homemaker, Bronze Age Homemaker, etc...and Homemaker population would produce Child populations in addition to other benefits. Over time, child populations would turn into Student populations that could acquire new skills.