We all know that current citizen-soldiers can work and build buildings, as well as fight.
This has been a major turn off for many people who came from Age of Empires and similar games. Instead of regurgitating all that's been said in the past, I'll just post a link to a comment that described it best:
https://news.ycombinator.com/item?id=32993448
So, I'll propose a system that's already present in some mods for the game, with a few caveats.
The major changes would include the following.
1) Citizen-soldiers are no longer citizens.
They are basic soldiers that can't gather any resource, but can still build some military buildings. Rationale is that this separates the responsibilities between your fighting units and economic units. This is a key trait that has defined RTS genre from the beginning.
2) Women are replaced by a "Citizen" unit that is randomly assigned a gender when created.
These citizens are your economic units. They can gather resources, build all buildings, repair, etc. They don't have different gather rates, the difference is cosmetic. They cost only 50 food, so you don't waste wood on building any gatherers in the early game. Obviously, this requires a new model for male citizens.
3) Common soldiers can only be trained at the Barracks, Stables or Archery Ranges.
Soldiers will not be able to build Civic Centers, nor should they be trainable from the Civic Centers. Some mercenary units that cost Metal could be made as an exception to this rule.
4) Common soldiers can still gain ranks as normal.
No change is required here. Players can choose to train cheaper, more expendable units, or spend more resources for champions.
I don't want to sound divisive, but the current model is very off-putting for someone who just wants to sit down and play a fun game. Different gather rates for females and male citizen-soldiers are the core of this issue. Why keep this feature and needlessly complicate the player's decision making in the early game? The player should gain options as he/she advances through the phases, builds up their town, researches upgrades. Not immediately at the start. Not to mention the balance considerations, the needless code that went into implementing a very questionable design decision. Even from the historical standpoint.
Thank you for reading all this. If not, here's a TL:DR:
Citizen-soldiers are an outdated concept, that has needlessly complicated the gameplay of this very promising RTS game for so long. The player must have a clear decision-tree at the start of each game, and gain options as he/she advances through the phases. The player shouldn't be punished for making gatherers (the wood cost). There should be a clear distinction between economic and military units. A new "Citizen" unit could replace the female worker, with a new male model added for each civilization. Citizen-soldiers could become just basic, expendable troops.